>gi|26553585|ref|NP_757519.1| pseudouridine synthase [Mycoplasma penetrans HF-2] >gi|26453591|dbj|BAC43923.1| pseudouridine synthase [Mycoplasma penetrans HF-2] (298 aa)
Score = 1350, Expect = 2.6e-147, Identities = 298/298 (100%), Positives = 298/298 (100%)
  Q:     1 MKNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           MKNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK
  S:     1 MKNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
>gi|13357873|ref|NP_078147.1| pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum serovar 3 str. ATCC 700970] >gi|11279832|pir||H82907 pseudouridine synthase (uracil hydrolase) UU313 [imported] - Ureaplasma urealyticum >gi|6899289|gb|AAF30722.1|AE002128_10 pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum serovar 3 str. ATCC 700970] (299 aa)
Score = 450, Expect = 7.2e-43, Identities = 114/295 (38%), Positives = 175/295 (59%)
  Q:     1 MKNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEE-KIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVE--VDAPI-KRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + ++QR+D  +    + SR++ K  ++ NL+ VN   ISK +  + +   I +  E  IV+E K L P+   +EI++ED+ +LIVNKP+ ++VHPTS+   NTLAN +KY   +             I HRLDK T GL+I+ K+  + N+  + F+ + I K Y A++HN    + +   ++ PI    +   R +     + KEA +I K + +YKN  L EV + TGRTHQIRVH  +I + V NDP+YG  KH   TT+Y QYL ++ + F HP T K+V   ++MPKEF E I++
  S:     7 LMSSQRIDKFLVENTNYSRTLIKKMLDQNLILVNDNFISKASYLLKKNDYIQINNELPIVQEQKKLLPFVYSLEIIFEDQDLLIVNKPSGMLVHPTSFHEQNTLANALKYYLKTDNFY---------ITHRLDKNTSGLIIICKNQIALNSLQQQFMQKTIRKSYYAIVHNRFDMQHLHFMINEPIGHSYQDKLRMKTGNSKNTKEAISIVKVLEQYKNTALVEVSIITGRTHQIRVHMRYINHPVYNDPLYGISKH---TTEYEQYLHSFYISFNHPSTNKKVEFKINMPKEFMELIRE 294
>gi|167971859|ref|ZP_02554136.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum serovar 6 str. ATCC 27818] >gi|168282520|ref|ZP_02690187.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum serovar 14 str. ATCC 33697] >gi|168308674|ref|ZP_02691349.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum serovar 1 str. ATCC 27813] >gi|170762382|ref|YP_001752395.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum serovar 3 str. ATCC 27815] >gi|168827959|gb|ACA33221.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum serovar 3 str. ATCC 27815] >gi|171902645|gb|EDT48934.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum serovar 1 str. ATCC 27813] >gi|182675832|gb|EDT87737.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum serovar 14 str. ATCC 33697] >gi|186700803|gb|EDU19085.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum serovar 6 str. ATCC 27818] (292 aa)
Score = 449, Expect = 8.4e-43, Identities = 114/293 (38%), Positives = 174/293 (59%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEE-KIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVE--VDAPI-KRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           ++QR+D  +    + SR++ K  ++ NL+ VN   ISK +  + +   I +  E  IV+E K L P+   +EI++ED+ +LIVNKP+ ++VHPTS+   NTLAN +KY   +             I HRLDK T GL+I+ K+  + N+  + F+ + I K Y A++HN    + +   ++ PI    +   R +     + KEA +I K + +YKN  L EV + TGRTHQIRVH  +I + V NDP+YG  KH   TT+Y QYL ++ + F HP T K+V   ++MPKEF E I++
  S:     2 SSQRIDKFLVENTNYSRTLIKKMLDQNLILVNDNFISKASYLLKKNDYIQINNELPIVQEQKKLLPFVYSLEIIFEDQDLLIVNKPSGMLVHPTSFHEQNTLANALKYYLKTDNFY---------ITHRLDKNTSGLIIICKNQIALNSLQQQFMQKTIRKSYYAIVHNRFDMQHLHFMINEPIGHSYQDKLRMKTGNSKNTKEAISIVKVLEQYKNTALVEVSIITGRTHQIRVHMRYINHPVYNDPLYGISKH---TTEYEQYLHSFYISFNHPSTNKKVEFKINMPKEFMELIRE 287
>gi|15828769|ref|NP_326129.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate synthase) (Uracil hydrolyase) [Mycoplasma pulmonis UAB CTIP] >gi|14089712|emb|CAC13471.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE D (PSEUDOURIDYLATE SYNTHASE) (URACIL HYDROLYASE) [Mycoplasma pulmonis] (296 aa)
Score = 446, Expect = 2.0e-42, Identities = 112/292 (38%), Positives = 175/292 (59%)
  Q:     2 KNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPN--TKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           K ++R+D  +S   ++SR+  K  I    V VNGK+I KPN   K D E E+I    K++++T  L P K D++IVYED++++++NKP+ ++VHP     S TL N + Y F  K +      LR GIVHR+DK T GL+I+AK+        K+  + +I++ Y+A++    + + V ++ PI R +   ++    + ++K A T    I ++    +  +L E +L TGRTHQIRVH  + K+ V NDP+YG       + YGQYL AYKL F+HP T +E+   + MP+EF+  I
  S:     7 KYSERIDKYISDNSAISRNDIKSLILEKAVFVNGKVIQKPNFILKPDAEIEVI----KVIDKTIDLKPEKMDLDIVYEDEHLIVINKPSGLVVHPAPGHYSQTLVNGLIYHF--KNLSNENGLLRPGIVHRIDKDTSGLLIIAKTNQVHQLLAKMLKNHEIKRSYIAIVEGFFENKIVHLNLPIGRSQKDRKKMEITNNNSKNAITHVYLIKQFYYEKQPLSLVECQLETGRTHQIRVHLNYFKHPVWNDPLYGKSF----SDYGQYLHAYKLFFVHPITNQELTFEIPMPEEFQRII 294
>gi|42561113|ref|NP_975564.1| ribosomal large subunit pseudouridylate synthase D [Mycoplasma mycoides subsp. mycoides SC str. PG1] >gi|42492610|emb|CAE77206.1| ribosomal large subunit pseudouridylate synthase D [Mycoplasma mycoides subsp. mycoides SC str. PG1] (310 aa)
Score = 435, Expect = 3.9e-41, Identities = 110/295 (37%), Positives = 183/295 (62%)
  Q:     1 MKNTQRLDILVS---SKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +  T RLD L+    + +  SRS  +  I+   ++VN +II+  N  V   S+I +  +  + +  ++   + D++I+Y+D  +L++NK N+I VHP+  + +NT+ N +    D +    NG+ LR GIVHR+DK T GL+IVAK+  +    +++F + +I K+YLA++   ++     +DAPI R +T  ++      ++K+A T F+ + ++   TL + ++ TGRTHQIRVH  +I + V+NDP+YG KH  + T +GQYL AYKLKF HP T+KE+ +   +PKEF + IK+
  S:     9 LNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFLVKPNSQITITIKDPILDPNLVKNDEIDLDIIYQDDDLLVINKQNNITVHPSLNNTNNTIVNAL-LASDVELSSINGE-LRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIVTGVIKPNKGLIDAPIGRSQTDRKKMSVTAKNSKQAITTFEVVERFFKNTLVKCQIQTGRTHQIRVHFNYINHPVLNDPVYGKKH-QEFTDFGQYLHAYKLKFTHPITKKEIELISPLPKEFDDKIKE 303
>gi|167925304|ref|ZP_02512395.1| ribosomal large subunit pseudouridylate synthase D [Mycoplasma mycoides subsp. mycoides LC str. GM12] (310 aa)
Score = 430, Expect = 1.2e-40, Identities = 108/295 (36%), Positives = 182/295 (61%)
  Q:     1 MKNTQRLDILVS---SKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +  T RLD L+    + +  SRS  +  I+   ++VN +II+  N  V   S+I +  +  + +  ++   + D++I+Y+D  +L++NK N+I VHP+  + +NT+ N +    D +    NG+ LR GIVHR+DK T GL+IVAK+  +    +++F + +I K+YLA++   ++     +DAPI R +   ++      ++K+A T F+ + ++   TL + ++ TGRTHQIRVH  +I + V+NDP+YG KH  + T +GQYL AYKL+F HP T+KE+ +   +PKEF + IK+
  S:     9 LNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFVVKPNSQITITIKDPILDPNLVKNDEIDLDIIYQDDDLLVINKQNNITVHPSLSNTNNTIVNAL-LASDVELSSINGE-LRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIVSGVIKPNKGLIDAPIGRSQIDRKKMSVTAKNSKQAITTFEVVERFLKNTLVKCQIQTGRTHQIRVHFNYINHPVLNDPVYGKKH-QEFTDFGQYLHAYKLRFTHPITKKEIELISPLPKEFDDKIKE 303
>gi|50365205|ref|YP_053630.1| 23S rRNA/tRNA pseudouridine synthase [Mesoplasma florum L1] >gi|50363761|gb|AAT75746.1| 23S rRNA/tRNA pseudouridine synthase [Mesoplasma florum L1] (311 aa)
Score = 423, Expect = 9.0e-40, Identities = 112/280 (40%), Positives = 169/280 (60%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           SRS  +  I++  V VNG + +K N  +  D E EI + E K    T  + P K D++IVYED  IL+VNKPN+++VHP + +   T+ N +    D++ +   G   R GIVHR+DK T GL+IVAK+  S    T++  + +I K+Y+AL+   ++     +DAPI R +   ++ +    ++K A T F+ I +    TL +  + TGRTHQIRVH  FIK+ ++NDP YG K   K T +GQ L AYKL+F+HP T++ V +  ++PKEF + I + G
  S:    27 SRSYIQTLIKDGNVIVNGNVETKQNFNLIGDIEIEINIPEVK----TSTINPEKIDLDIVYEDDDILVVNKPNNMVVHPGAGNTEGTMVNAL-LGRDAEFLSTIGGVERPGIVHRIDKQTTGLLIVAKNDKSHQVLTEMLKNHEIYKEYVALVWGEIKEDKGIIDAPIGRHQNDRKKMMVTSKNSKYAVTNFEVIKRLDKTTLVKCAIETGRTHQIRVHFNFIKHPIVNDPSYG-KLAEKQTDFGQMLHAYKLEFLHPITKEMVKLKAELPKEFTDKILQEG 302
>gi|171920977|ref|ZP_02696366.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 13 str. ATCC 33698] >gi|185179169|ref|ZP_02555823.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 5 str. ATCC 27817] >gi|188024223|ref|ZP_02570294.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 7 str. ATCC 27819] >gi|188039440|ref|ZP_02528398.2| pseudouridine synthase (uracil hydrolase) [Ureaplasma urealyticum serovar 8] >gi|188518627|ref|ZP_02556991.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 11 str. ATCC 33695] >gi|188524489|ref|ZP_02558401.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 12 str. ATCC 33696] >gi|188530877|ref|ZP_02546662.2| pseudouridine synthase (uracil hydrolase) [Ureaplasma urealyticum serovar 4 str. ATCC 27816] >gi|188568601|ref|ZP_02828475.2| pseudouridine synthase (uracil hydrolase) [Ureaplasma urealyticum serovar 2] >gi|195867617|ref|ZP_03079619.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 9 str. ATCC 33175] >gi|171903003|gb|EDT49292.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 13 str. ATCC 33698] >gi|184208903|gb|EDU05946.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 5 str. ATCC 27817] >gi|188018878|gb|EDU56918.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 7 str. ATCC 27819] >gi|188997853|gb|EDU66950.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 11 str. ATCC 33695] >gi|195659610|gb|EDX52990.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 12 str. ATCC 33696] >gi|195660674|gb|EDX53929.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar 9 str. ATCC 33175] (299 aa)
Score = 417, Expect = 4.3e-39, Identities = 107/296 (36%), Positives = 168/296 (56%)
  Q:     1 MKNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEK-IVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVE--VDAPIKRVETSTRREVSRDI-DAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           + + +R+D  +      SR+  K  +E NLV VN  II+K +  + +   + +K E+ +++  K L P+   +EIV+ED+ +L++NKP+ ++VHPTS+   NTLAN +K+   +             I HRLDK T GL+++ K+  +     + F+ + ++K Y A++HN      +   ++ PI        R  + D  +AKEA +I K I +Y+N  L EV + TGRTHQIRVH   I + + NDP+YG  KH   TT Y QYL ++ + FIHP T + V     MP EF   IK++
  S:     7 LTSPKRIDKFLVEVTDYSRTSIKKMLEQNLVLVNDNIITKQSYLLQKNDSVEIKNEQCVIDSQKELLPFACPLEIVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALKHYLKTDDFY---------ITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVHNRFDMHHLHFMINEPIGHSYQDKLRMKTGDAKNAKEAISIVKVIEQYQNTALVEVSIITGRTHQIRVHMRHINHPIYNDPLYGISKH---TTPYEQYLHSFYISFIHPSTNEIVEFKTLMPNEFINLIKEW 295
>gi|83319260|ref|YP_424375.1| ribosomal large subunit pseudouridine synthase A [Mycoplasma capricolum subsp. capricolum ATCC 27343] >gi|83283146|gb|ABC01078.1| ribosomal large subunit pseudouridine synthase, RluA family [Mycoplasma capricolum subsp. capricolum ATCC 27343] (322 aa)
Score = 417, Expect = 4.3e-39, Identities = 114/295 (38%), Positives = 181/295 (61%)
  Q:     1 MKNTQRLDILVS---SKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIIL------------KEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +  T RLD L+    + +  SRS  +  I+   ++VN +II+  N  V   S+II+            K +  V +  +      D+ I+Y+D  +L++NK N+I VHP+  + +NT+ N +    D +    NG+ LR GIVHR+DK T GL+IVAK+  +    +++F + +I K+YLA++   ++     +DAPI R +T  ++      ++K A T F+ + ++   TL + ++ TGRTHQIRVH  +I + V+NDPIYG KH  + T +GQYL AYKLKF HP T+KE+ +   +PKEF + IK+
  S:     9 VNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITSNNFLVKPNSQIIITIKDPVLDPNITKNKDPVLDPNITKNKDIDLNIIYQDDDLLVINKQNNITVHPSLNNTNNTIVNAL-LASDVELSSINGE-LRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIVTGVIKPNKGLIDAPIGRSQTDRKKMSVTAKNSKHAITTFEVVERFLKNTLIKCQIQTGRTHQIRVHFNYINHPVLNDPIYGKKH-QEFTDFGQYLHAYKLKFTHPITKKEIELISPLPKEFDDKIKE 315
>gi|164687826|ref|ZP_02211854.1| hypothetical protein CLOBAR_01470 [Clostridium bartlettii DSM 16795] >gi|164603101|gb|EDQ96566.1| hypothetical protein CLOBAR_01470 [Clostridium bartlettii DSM 16795] (307 aa)
Score = 413, Expect = 1.3e-38, Identities = 118/290 (40%), Positives = 169/290 (58%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKI-ISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD+ +SS+   +SRS  +  I++  V VNGKI  +K   K D+   I +   K++E    + P    I+IVYED  +LIVNKP D++VHP   +  NTL N I Y         NG  +R GIVHR+DK T G++++AK+ ++ N+  +   D  I ++Y  + H  ++   + VD PI R     R +++   D K A T F+ I +Y+NFT  +  L TGRTHQIRVHA  I + ++ DPIYGPK+ +K    GQ L A KL FIHP T++ V  N D+P  F E + K
  S:    21 RLDVYLSSQLGEMSRSYIQKIIKDKKVKVNGKIEKAKYAVKEDDSVVIEIPAPKLLE----VIPQDIPIDIVYEDDDLLIVNKPQDMVVHPAPGNYENTLVNAILYHCKDNLSSING-VIRPGIVHRIDKDTSGILMIAKNNNAHNSLAEQLKDHSITREYEFICHGVVKEDKITVDRPIGR-NPKDRLKMAIVKDGKRAVTHFEVIKRYENFTHMKANLETGRTHQIRVHAASIGHPLLGDPIYGPKN-SKIKCKGQTLHARKLGFIHPTTKQYVEFNSDLPDYFVEILNK 305
>gi|188592412|ref|ZP_02693821.2| pseudouridine synthase (uracil hydrolase) [Ureaplasma urealyticum serovar 10] (299 aa)
Score = 412, Expect = 1.5e-38, Identities = 106/296 (35%), Positives = 167/296 (56%)
  Q:     1 MKNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEK-IVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVE--VDAPIKRVETSTRREVSRDI-DAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           + + +R+D  +      SR+  K  +E NLV VN  II+K +  + +   + +K E+ +++  K L P+   +EIV+ED+ +L++NKP+ ++VHPTS+   NTLAN +K+   +             I HRLDK T GL+++ K+  +     + F+ + ++K Y A++HN      +   ++ PI        R  + D  + KEA +I K I +Y+N  L EV + TGRTHQIRVH   I + + NDP+YG  KH   TT Y QYL ++ + FIHP T + V     MP EF   IK++
  S:     7 LTSPKRIDKFLVEVTDYSRTSIKKMLEQNLVLVNDNIITKQSYLLQKNDSVEIKNEQCVIDSQKELLPFACPLEIVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALKHYLKTDDFY---------ITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVHNRFDMHHLHFMINEPIGHSYQDKLRMKTGDAKNVKEAISIVKVIEQYQNTALVEVSIITGRTHQIRVHMRHINHPIYNDPLYGISKH---TTPYEQYLHSFYISFIHPSTNEIVEFKTLMPNEFINLIKEW 295
>gi|162447675|ref|YP_001620807.1| ribosomal large subunit pseudouridine synthase, RluA-like protein [Acholeplasma laidlawii PG-8A] >gi|161985782|gb|ABX81431.1| ribosomal large subunit pseudouridine synthase, RluA-like protein [Acholeplasma laidlawii PG-8A] (297 aa)
Score = 412, Expect = 1.5e-38, Identities = 109/296 (36%), Positives = 166/296 (56%)
  Q:     2 KNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +   RLD  + +   L+RS     I++ LV VNG + +K   K+    EI L  E   EET  L P   D+ IVYED  I+++NKP  ++VHP+      TL + + +  D+    +N DPLR GI+HR+DK T GL++VAK+ ++     +      I+++Y+AL+   L      +DAPI R     R +++     K A T F+ +  +++ TL   +L TGRTHQIRVH  +IK+ V  DP+YG K   K  K GQ L A++L+F+HP T+K + +   +P EF+ Y+   G
  S:     8 QTDSRLDHFLVASTELNRSQITTLIKDGLVMVNG-LTTKAGYKLKNSDEITLNLEA-KEETNPLKPKNIDLNIVYEDDDIMVINKPKGLVVHPSETFSETTLVSGLLHHTDTLS-THNDDPLRPGILHRIDKDTSGLILVAKTNEAHKILAQDLKSHDIKREYIALVEGVLDHNKGVIDAPIAR-HPKIRTKMAVVATGKPAITHFEVMRTFRDHTLLHCKLETGRTHQIRVHLAYIKHPVTGDPLYGTK--AKILKDGQLLHAFRLEFVHPITKKVMMLEAPLPPEFESYLVTLG 297
>gi|55820603|ref|YP_139045.1| ribosomal large subunit pseudouridine synthase D [Streptococcus thermophilus LMG 18311] >gi|55736588|gb|AAV60230.1| ribosomal large subunit pseudouridine synthase D [Streptococcus thermophilus LMG 18311] (296 aa)
Score = 412, Expect = 1.6e-38, Identities = 114/293 (38%), Positives = 168/293 (57%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII---LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  ++    LSRS A   I+   V VNGK  S     V +E ++I   L EE+++E      P    ++I+YED  + +VNKP  ++VHP++   S TL N + Y    K +      +R GIVHR+DK T GL+++AK+  + NA      D+K  +KY+A++H +L      ++API R +   R++ +     K A T F  + ++ N+TL E++L TGRTHQIRVH  +I + V  DP+YGP+   KT K +GQ+L A  L F HP T K V  N + P  FKE ++K  K
  S:    11 RLDKSLADLTELSRSQANEAIKAGTVLVNGK--SAKAKYVVKEGDVITYVLPEEEVLEYKAEDIP----LDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMY--HVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD-RKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR---KTLKGHGQFLHAKTLGFTHPTTGKLVEFNAEEPIIFKETLEKLRK 295
>gi|148984670|ref|ZP_01817938.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP3-BS71] >gi|149006397|ref|ZP_01830109.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP18-BS74] >gi|147762174|gb|EDK69136.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP18-BS74] >gi|147923061|gb|EDK74176.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP3-BS71] (295 aa)
Score = 412, Expect = 1.6e-38, Identities = 114/293 (38%), Positives = 174/293 (59%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  +S    LSRS+A  +I++  V VNG++  K      +E +++      V E +VL    +D+  EIVY+D+ + +VNKP  ++VHP++   S TL N + Y I D   I  NG  LR GIVHR+DK T GL+++AK+ D+  A  +   D+K  +KY A++H +L      ++API R E   R++ +     K A T F  + ++ +++L E++L TGRTHQIRVH  +I + V  D +YGP+   KT K +GQ+L A  L F HP T K +    D+P+ FKE +++  K
  S:    11 RLDKALSDLSELSRSLANEQIKSGQVLVNGQV--KKAKYTVQEGDVVTYH---VPEPEVLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGI--NG-VLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSVAGDEVYGPR---KTLKGHGQFLHAKTLGFTHPRTGKTLEFKADIPEIFKETLERLRK 295
>gi|148996979|ref|ZP_01824633.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP11-BS70] >gi|168491017|ref|ZP_02715160.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Streptococcus pneumoniae CDC0288-04] >gi|168575592|ref|ZP_02721528.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Streptococcus pneumoniae MLV-016] >gi|147756679|gb|EDK63719.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP11-BS70] >gi|183574680|gb|EDT95208.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Streptococcus pneumoniae CDC0288-04] >gi|183578513|gb|EDT99041.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Streptococcus pneumoniae MLV-016] (295 aa)
Score = 411, Expect = 2.3e-38, Identities = 114/293 (38%), Positives = 174/293 (59%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  +S    LSRS+A  +I++  V VNG++  K      +E +++      V E +VL    +D+  EIVY+D+ + +VNKP  ++VHP++   S TL N + Y I D   I  NG  LR GIVHR+DK T GL+++AK+ D+  A  +   D+K  +KY A++H +L      ++API R E   R++ +     K A T F  + ++ +++L E++L TGRTHQIRVH  +I + V  D +YGP+   KT K +GQ+L A  L F HP T K +    D+P+ FKE +++  K
  S:    11 RLDKALSDLTELSRSLANEQIKSGQVLVNGQV--KKAKYTVQEGDVVTYH---VPEPEVLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGI--NG-VLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR---KTLKGHGQFLHAKTLGFTHPRTGKTLEFKADIPEIFKETLERLRK 295
>gi|15900809|ref|NP_345413.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae TIGR4] >gi|111658131|ref|ZP_01408829.1| hypothetical protein SpneT_02000697 [Streptococcus pneumoniae TIGR4] >gi|148992939|ref|ZP_01822558.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP9-BS68] >gi|149010429|ref|ZP_01831800.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP19-BS75] >gi|168485879|ref|ZP_02710387.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae CDC1087-00] >gi|168490255|ref|ZP_02714454.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP195] >gi|169834331|ref|YP_001694382.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae Hungary19A-6] >gi|182683874|ref|YP_001835621.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae CGSP14] >gi|194398681|ref|YP_002037566.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae G54] >gi|14972404|gb|AAK75053.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae TIGR4] >gi|147764910|gb|EDK71839.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP19-BS75] >gi|147928391|gb|EDK79407.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP9-BS68] >gi|168996833|gb|ACA37445.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae Hungary19A-6] >gi|182629208|gb|ACB90156.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae CGSP14] >gi|183571050|gb|EDT91578.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae CDC1087-00] >gi|183571388|gb|EDT91916.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP195] >gi|194358348|gb|ACF56796.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae G54] (295 aa)
Score = 411, Expect = 2.3e-38, Identities = 114/293 (38%), Positives = 174/293 (59%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  +S    LSRS+A  +I++  V VNG++  K      +E +++      V E +VL    +D+  EIVY+D+ + +VNKP  ++VHP++   S TL N + Y I D   I  NG  LR GIVHR+DK T GL+++AK+ D+  A  +   D+K  +KY A++H +L      ++API R E   R++ +     K A T F  + ++ +++L E++L TGRTHQIRVH  +I + V  D +YGP+   KT K +GQ+L A  L F HP T K +    D+P+ FKE +++  K
  S:    11 RLDKALSDLSELSRSLANEQIKSGQVLVNGQV--KKAKYTVQEGDVVTYH---VPEPEVLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGI--NG-VLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR---KTLKGHGQFLHAKTLGFTHPRTGKTLEFKADIPEIFKETLERLRK 295
>gi|16801023|ref|NP_471291.1| hypothetical protein lin1957 [Listeria innocua Clip11262] >gi|16414458|emb|CAC97187.1| lin1957 [Listeria innocua] (302 aa)
Score = 410, Expect = 2.9e-38, Identities = 107/290 (36%), Positives = 171/290 (58%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D +++     SRS  +  ++N  +TVNG++ +KPN KV    EI   E +  EE ++L    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ I +   +TL   +L TGRTHQIRVH ++I + +  DP YGPK  N     GQ+L A KL F HP T + +     +P  F++ +K
  S:    15 ERVDKVIAEMMEKSRSAIQLMLKNGDITVNGEL-AKPNYKVQVGDEI-RYEAREPEELEILA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVIERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQFLHAAKLGFDHPTTNERMTFEAPLPDSFEQALK 296
>gi|116873278|ref|YP_850059.1| ribosomal large subunit pseudouridine synthase [Listeria welshimeri serovar 6b str. SLCC5334] >gi|116742156|emb|CAK21280.1| rluD [Listeria welshimeri serovar 6b str. SLCC5334] (302 aa)
Score = 410, Expect = 3.3e-38, Identities = 108/290 (37%), Positives = 171/290 (58%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D +++     SRS  +  ++N  +TVNG++ +KPN KV    EI   E +  EE +VL    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ + +   +TL   +L TGRTHQIRVH ++I + +  DP YGPK  N     GQYL A KL F HP T + +     +P  F++ +K
  S:    15 ERVDKVIAEMMGKSRSAIQLMLKNGDITVNGEL-AKPNYKVQVGDEIHY-EIREPEELEVLA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQYLHAAKLGFDHPTTNERMTFEAPLPASFEKALK 296
>gi|116627406|ref|YP_820025.1| ribosomal large subunit pseudouridine synthase D [Streptococcus thermophilus LMD-9] >gi|116100683|gb|ABJ65829.1| ribosomal large subunit pseudouridine synthase D [Streptococcus thermophilus LMD-9] (296 aa)
Score = 408, Expect = 4.7e-38, Identities = 113/293 (38%), Positives = 167/293 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEI--ILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  ++    LSRS A   I+   V VNGK+ +K    V E   I  +L EE+++E      P    ++I+YED  + +VNKP  I+VHP++   S TL N + Y    K +      +R GIVHR+DK T GL+++AK+  + NA      D+K  +KY+A++H +L      ++API R +   R++ +     K A T F  + ++ N+TL E++L TGRTHQIRVH  +I + V  DP+YGP+   KT K +GQ+L A  L F HP T + V    + P  FKE ++K  K
  S:    11 RLDKSLADLTELSRSQANEAIKAGTVLVNGKL-AKAKYVVKEGDVITYVLPEEEVLEYKAEDIP----LDIIYEDADVAVVNKPQGIVVHPSAGHTSGTLVNALMY--HVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD-RKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR---KTLKGHGQFLHAKTLGFTHPTTGELVEFTAEEPIIFKETLEKLRK 295
>gi|168494358|ref|ZP_02718501.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Streptococcus pneumoniae CDC3059-06] >gi|183575636|gb|EDT96164.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Streptococcus pneumoniae CDC3059-06] (295 aa)
Score = 407, Expect = 5.9e-38, Identities = 113/293 (38%), Positives = 173/293 (59%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  +S    LSRS+A  +I++  V VNG++  K      +E +++      V E +VL    +D+  EIVY+D+ + +VNKP  ++VHP++   S TL N + Y I D   I  NG  LR GIVHR+DK T GL+++AK+ D+     +   D+K  +KY A++H +L      ++API R E   R++ +     K A T F  + ++ +++L E++L TGRTHQIRVH  +I + V  D +YGP+   KT K +GQ+L A  L F HP T K +    D+P+ FKE +++  K
  S:    11 RLDKALSDLSELSRSLANEQIKSGQVLVNGQV--KKAKYTVQEGDVVTYH---VPEPEVLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGI--NG-VLRPGIVHRIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSVAGDEVYGPR---KTLKGHGQFLHAKTLGFTHPRTGKTLEFKADIPEIFKETLERLRK 295
>gi|16803883|ref|NP_465368.1| hypothetical protein lmo1843 [Listeria monocytogenes EGD-e] >gi|47097693|ref|ZP_00235203.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Listeria monocytogenes str. 1/2a F6854] >gi|153175073|ref|ZP_01930468.1| hypothetical protein LMIG_00487 [Listeria monocytogenes FSL N3-165] >gi|153183332|ref|ZP_01934192.1| hypothetical protein LMOG_00044 [Listeria monocytogenes J0161] >gi|153191347|ref|ZP_01938567.1| hypothetical protein LMPG_00585 [Listeria monocytogenes J2818] >gi|153196351|ref|ZP_01940721.1| hypothetical protein LMRG_00990 [Listeria monocytogenes 10403S] >gi|16411297|emb|CAC99921.1| lmo1843 [Listeria monocytogenes] >gi|47013931|gb|EAL04954.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Listeria monocytogenes str. 1/2a F6854] >gi|126943623|gb|EBA21340.1| hypothetical protein LMOG_00044 [Listeria monocytogenes J0161] >gi|127633812|gb|EBA23204.1| hypothetical protein LMRG_00990 [Listeria monocytogenes 10403S] >gi|127765126|gb|EBA25476.1| hypothetical protein LMPG_00585 [Listeria monocytogenes J2818] >gi|133729526|gb|EBA31224.1| hypothetical protein LMIG_00487 [Listeria monocytogenes FSL N3-165] (303 aa)
Score = 407, Expect = 6.5e-38, Identities = 107/290 (36%), Positives = 171/290 (58%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D +++     SRS  +  ++N  +TVNG++ +KPN KV    EI   E +  EE +VL    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ + +   +TL   +L TGRTHQIRVH ++I + +  DP YGPK  N     GQ+L A KL F HP T + +     +P  F++ +K
  S:    15 ERVDKVIAEMMGKSRSAIQLMLKNGDITVNGEL-AKPNYKVQVGDEIHY-EVREPEELEVLA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQFLHAAKLGFDHPTTNERMTFEAPLPSSFEKALK 296
>gi|167212577|ref|ZP_02282884.1| hypothetical protein LmonL_16655 [Listeria monocytogenes LO28] >gi|167404774|ref|ZP_02309551.1| hypothetical protein LmonocytFSL_15226 [Listeria monocytogenes FSL J2-003] (302 aa)
Score = 407, Expect = 6.6e-38, Identities = 107/290 (36%), Positives = 171/290 (58%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D +++     SRS  +  ++N  +TVNG++ +KPN KV    EI   E +  EE +VL    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ + +   +TL   +L TGRTHQIRVH ++I + +  DP YGPK  N     GQ+L A KL F HP T + +     +P  F++ +K
  S:    15 ERVDKVIAEMMGKSRSAIQLMLKNGDITVNGEL-AKPNYKVQVGDEIHY-EVREPEELEVLA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQFLHAAKLGFDHPTTNERMTFEAPLPSSFEKALK 296
>gi|15902874|ref|NP_358424.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae R6] >gi|116515398|ref|YP_816303.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae D39] >gi|148988365|ref|ZP_01819812.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP6-BS73] >gi|168482999|ref|ZP_02707951.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Streptococcus pneumoniae CDC1873-00] >gi|15458431|gb|AAK99634.1| 23S rRNA pseudouridine synthase (supresses ftsH(ts) mutants) [Streptococcus pneumoniae R6] >gi|116075974|gb|ABJ53694.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae D39] >gi|147926046|gb|EDK77120.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP6-BS73] >gi|172043419|gb|EDT51465.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Streptococcus pneumoniae CDC1873-00] (295 aa)
Score = 406, Expect = 7.6e-38, Identities = 113/293 (38%), Positives = 173/293 (59%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  +S    LSRS+A  +I++  V VNG++  K      +E +++      V E +VL    +D+  EIVY+D+ + +VNKP  ++VHP++   S TL N + Y I D   I  NG  LR GIVHR+DK T GL+++AK+ D+     +   D+K  +KY A++H +L      ++API R E   R++ +     K A T F  + ++ +++L E++L TGRTHQIRVH  +I + V  D +YGP+   KT K +GQ+L A  L F HP T K +    D+P+ FKE +++  K
  S:    11 RLDKALSDLSELSRSLANEQIKSGQVLVNGQV--KKAKYTVQEGDVVTYH---VPEPEVLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGI--NG-VLRPGIVHRIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR---KTLKGHGQFLHAKTLGFTHPRTGKTLEFKADIPEIFKETLERLRK 295
>gi|167344070|ref|ZP_02289911.1| hypothetical protein LmonocyFSL_13863 [Listeria monocytogenes FSL J1-208] (328 aa)
Score = 406, Expect = 7.8e-38, Identities = 107/290 (36%), Positives = 172/290 (59%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D +++     SRS  +  ++N  +TVNG++ +KPN KV    EI   E +  EE +VL    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ + +   +TL + +L TGRTHQIRVH ++I + +  DP YGPK  N     GQ+L A KL F HP T + +     +P  F++ +K
  S:    15 ERVDKVIAEMMGKSRSAIQLMLKNGDITVNGEL-AKPNYKVQVGDEIHY-EVREPEELEVLA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVLERLPGYTLIKCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQFLHAAKLGFDHPTTNERMTFEAPLPNSFEKALK 296
>gi|125717901|ref|YP_001035034.1| ribosomal large subunit pseudouridine synthase D, putative [Streptococcus sanguinis SK36] >gi|125497818|gb|ABN44484.1| Ribosomal large subunit pseudouridine synthase D, putative [Streptococcus sanguinis SK36] (298 aa)
Score = 406, Expect = 8.2e-38, Identities = 110/291 (37%), Positives = 172/291 (59%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII---LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           QRLD  V+    LSRS+A  +I++  + VNG+  +K      +E ++I   L E ++VE      P    +EIVY+D+ + ++NKP  ++VHP++   S TL N + Y I D   I  NG  LR GIVHR+DK T GL+++AK+  +  A      D+K  +KY A++H +L      ++API R E   R++ +     K A T F+ + ++ +++L E++L TGRTHQIRVH  +I + V  D +YGP+   KT K +GQ+L A  L F HP T + +    ++P  F+E ++K
  S:    12 QRLDKAVAELTDLSRSLANEQIKDGRILVNGQ--AKKAKYAVKEGDVISYELPEPEVVEYVAEDIP----LEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGI--NG-VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR---KTLKGHGQFLHARTLGFTHPRTGEVLEFTAEVPAIFQETLEK 294
>gi|46908075|ref|YP_014464.1| ribosomal large subunit pseudouridine synthase D [Listeria monocytogenes str. 4b F2365] >gi|47094208|ref|ZP_00231922.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Listeria monocytogenes str. 4b H7858] >gi|153167686|ref|ZP_01927790.1| hypothetical protein LMHG_00612 [Listeria monocytogenes FSL N1-017] >gi|167015014|ref|ZP_02277547.1| ribosomal large subunit pseudouridine synthase, RluD subfamily protein [Listeria monocytogenes FSL J1-194] >gi|167454405|ref|ZP_02320628.1| ribosomal large subunit pseudouridine synthase, RluD subfamily protein [Listeria monocytogenes FSL J2-064] >gi|46881345|gb|AAT04641.1| ribosomal large subunit pseudouridine synthase, RluA family [Listeria monocytogenes str. 4b F2365] >gi|47017415|gb|EAL08234.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Listeria monocytogenes str. 4b H7858] >gi|133726785|gb|EBA28483.1| hypothetical protein LMHG_00612 [Listeria monocytogenes FSL N1-017] (303 aa)
Score = 406, Expect = 8.5e-38, Identities = 107/290 (36%), Positives = 172/290 (59%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D +++     SRS  +  ++N  +TVNG++ +KPN KV    EI   E +  EE +VL    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ + +   +TL   +L TGRTHQIRVH ++I + +  DP YGPK  N     GQ+L A KL F HP T++ +     +P  F++ +K
  S:    15 ERVDKVIAEMMGKSRSAIQLMLKNGDITVNGEL-AKPNYKVQVGDEIHY-EVREPEELEVLA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQFLHAAKLGFDHPTTKERMMFEAPLPSSFEKALK 296
>gi|171778236|ref|ZP_02919442.1| hypothetical protein STRINF_00281 [Streptococcus infantarius subsp. infantarius ATCC BAA-102] >gi|171282936|gb|EDT48360.1| hypothetical protein STRINF_00281 [Streptococcus infantarius subsp. infantarius ATCC BAA-102] (298 aa)
Score = 404, Expect = 1.6e-37, Identities = 111/290 (38%), Positives = 167/290 (57%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  ++    LSRS A  +I+   V VNGK + +K   KV +     + EE+++E      P    ++IVYED+ + +V KP  ++VHP++   S TL N + Y I D   I  NG  +R GIVHR+DK T GL+++AK+  + NA      D+K  +KY+A++H ++      ++API R E   R++ +     K A T FK + ++ N+TL E+ L TGRTHQIRVH  +I + V  DP+YGP+   K    GQ+L A  L F HP T + +    ++P  FKE ++K
  S:    11 RLDKALADLTDLSRSQANDEIKKGTVLVNGKAVKAKYAVKVGDVVTYEVPEEEVLEYKAENIP----LDIVYEDEDVAVVYKPQGMVVHPSAGHTSGTLVNALMYHIKDLSSI--NG-VIRPGIVHRIDKDTSGLLMIAKNDTAHNALAAELKDKKSLRKYVAIVHGNIPNDRGVIEAPIGRSEKD-RKKQAVTAKGKPAVTHFKVLERFGNYTLVELTLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGN--GQFLHAQTLGFTHPKTGETMTFTAEVPVIFKETLEK 292
>gi|148377937|ref|YP_001256813.1| ribosomal large subunit pseudouridine synthaseD [Mycoplasma agalactiae PG2] >gi|148291983|emb|CAL59375.1| Ribosomal large subunit pseudouridine synthaseD [Mycoplasma agalactiae PG2] (305 aa)
Score = 403, Expect = 1.7e-37, Identities = 107/289 (37%), Positives = 170/289 (58%)
  Q:     1 MKNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNG-KIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           +K  +R+D  +S    ++R+ AK  IE   V V+  K + KPN  V E   +++   +++E+   +      ++I YED+Y+LI+NKP+ ++VHP    L++TL N + Y F +     NG  LR+GIVHR+DK T GL+I+AK  ++ N   K+  + +I++ YLA+    L  +T +++ PI+R +T  R+ +S   D K + T    +  +    K ++L + EL TGRTHQIRVH  +IK+ V  D IYG        ++ Q L AYKL F+HP   K + +  D+PKEF
  S:     6 VKYKERIDKYISDNSEITRNDAKALIEQEAVYVDDRKFVRKPNYMVREG--MVITVLRLLEKESNIEAVDMPLDIRYEDEYLLILNKPSGLVVHPAPGHLNDTLVNALMYHFKNNLSDANG-LLRLGIVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYLAICEGILPNKTTKINLPIQR-DTKNRKLMSIHKDGKSSVTYVHMLKSFYIDNKPYSLVKCELETGRTHQIRVHLAYIKHPVYGDSIYG----KSVDEFNQRLHAYKLSFMHPVINKLIEVYSDIPKEF 291
>gi|153202840|ref|ZP_01944278.1| hypothetical protein LMSG_01048 [Listeria monocytogenes HPB2262] >gi|133734910|gb|EBA36608.1| hypothetical protein LMSG_01048 [Listeria monocytogenes HPB2262] (294 aa)
Score = 403, Expect = 2.0e-37, Identities = 106/287 (36%), Positives = 170/287 (59%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +R+D +++     SRS  +  ++N  +TVNG++ +KPN KV    EI   E +  EE +VL    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ + +   +TL   +L TGRTHQIRVH ++I + +  DP YGPK  N     GQ+L A KL F HP T++ +     +P  F++
  S:    15 ERVDKVIAEMMGKSRSAIQLMLKNGDITVNGEL-AKPNYKVQVGDEIHY-EVREPEELEVLA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQFLHAAKLGFDHPTTKERMMFEAPLPSSFEK 293
>gi|168266249|ref|ZP_02688214.1| hypothetical protein LmonFSL_11664 [Listeria monocytogenes FSL J2-071] (302 aa)
Score = 403, Expect = 2.1e-37, Identities = 106/290 (36%), Positives = 171/290 (58%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D +++     SRS  +  +++  +TVNG++ +KPN KV    EI   E +  EE +VL    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ + +   +TL   +L TGRTHQIRVH ++I + +  DP YGPK  N     GQ+L A KL F HP T + +     +P  F++ +K
  S:    15 ERVDKVIAEMMGKSRSAIQLMLKSGDITVNGEL-AKPNYKVQVGDEIHY-EVREPEELEVLA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQFLHAAKLGFDHPTTNERMTFEAPLPSSFEKALK 296
>gi|13508031|ref|NP_109980.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma pneumoniae M129] >gi|2501680|sp|P75485|Y292_MYCPN Uncharacterized RNA pseudouridine synthase MG209 homolog (RNA-uridine isomerase) (RNA pseudouridylate synthase) >gi|1674240|gb|AAB96191.1| ribosomal large subunit pseudouridine synthase D-like protein [Mycoplasma pneumoniae M129] (309 aa)
Score = 402, Expect = 2.4e-37, Identities = 106/287 (36%), Positives = 166/287 (57%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILK-EEKIVEETKV-LTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTR--REVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           QRLD  +++  +LSR      I + LV+VNGK I+K    V  E  + +   E++ E+  V + P+   ++I+YED+ I++VNKPN +I HPTS++ S +L         +     N  P+ +  VHRLD+ T G++++AK+  S     K    + +++ YLAL+H  L + +  + AP++RV  +    +  +    AK A T F  +N+ +   L + EL TGRTHQIRVH +FIK+ V NDP+YG K   + T+YGQYL A ++ FIHP   KE+     + K F +
  S:    11 QRLDTFLATLLNLSRVKVAKLIVDGLVSVNGKKITKNGWLVQPEDRVHVNWSEELFEKVPVEVQPYDFPLDILYEDEQIMVVNKPNGLISHPTSFNESESL-------LGAALFHCNHQPVFL--VHRLDRDTSGVIMLAKNQSSLLHLQKQLQQRVMKRYYLALVHFPLDSLSGTISAPLERVGNNKVMWKVGNSSNKAKNAFTKFTVLNQNEKAALIKCELLTGRTHQIRVHLQFIKHPVYNDPLYGLKS-EQATEYGQYLHAQQISFIHPTLNKEMGFEAQLDKTFSD 291
>gi|167214706|ref|ZP_02285013.1| ribosomal large subunit pseudouridine synthase, RluD subfamily protein [Listeria monocytogenes FSL R2-503] (329 aa)
Score = 401, Expect = 3.1e-37, Identities = 107/290 (36%), Positives = 171/290 (58%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D +++     SRS  +  ++N  +TVNG++ +KPN KV    EI   E +  EE +VL    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ + +   +TL   +L TGRTHQIRVH ++I + +  DP YGPK  N     GQ+L A KL F HP T++ +     +P  F++  K
  S:    15 ERVDKVIAEMMGKSRSAIQLMLKNGDITVNGEL-AKPNYKVQVGDEIHY-EVREPEELEVLA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQFLHAAKLGFDHPTTKERMMFEAPLPSSFEKDFK 296
>gi|19745906|ref|NP_607042.1| hypothetical protein spyM18_0889 [Streptococcus pyogenes MGAS8232] >gi|19748060|gb|AAL97541.1| conserved hypothetical protein [Streptococcus pyogenes MGAS8232] (296 aa)
Score = 400, Expect = 3.8e-37, Identities = 107/290 (36%), Positives = 169/290 (58%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII---LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++    LSR  A  +I+  LV VNG+   K      +  ++I   L +E+++E      P    ++I+YED  + I+NKP  ++VHP++   S T+ N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +  A T+    +K  +KYLA++H +L      ++API R E   R++ +     KEA T F  + ++ +++L E++L TGRTHQIRVH  +I + V  DP+YGP+     + +GQ+L A  L   HP T KE+   ++ P+ F++ +K
  S:    10 QRLDKALADLSPLSRGQANDQIKQGLVLVNGQ--QKKAKYTVQAGDVICFELPKEEVLEYQAQNIP----LDIIYEDDALAIINKPQGMVVHPSAGHPSETMVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKTDAAHQALTEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKD-RKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR--KTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLK 291
>gi|145953052|ref|ZP_01802060.1| hypothetical protein CdifQ_04003029 [Clostridium difficile QCD-32g58] (429 aa)
Score = 399, Expect = 5.0e-37, Identities = 113/290 (38%), Positives = 165/290 (56%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLDI ++ +   +SRS  +  I++  V VN K+  K    V EE  I+++    + E KVL    +DI  +IVYED  +LI+NKP D++VHP   +  NTL N I Y    K    NG  +R GIVHR+DK T GL+++AK+  + N   +   +  I ++Y  + +  ++   + VD PI R     R +++   D K A T F+ + ++  FT     L TGRTHQIRVHA  I + ++ D +YGPK      K GQ L A KL FIHP T++ +  N ++P+ FKE IKK
  S:   143 RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKV-EKAKYLVKEEDNIVIE----IPEPKVLEVLPQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSING-VIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGR-NPKDRLKMAVVKDGKNAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLLGDFVYGPKETKFKLK-GQTLHAKKLGFIHPTTKEYIEFNSELPEYFKEAIKK 427
>gi|146318440|ref|YP_001198152.1| YlyB [Streptococcus suis 05ZYH33] >gi|145689246|gb|ABP89752.1| YlyB [Streptococcus suis 05ZYH33] (309 aa)
Score = 399, Expect = 5.6e-37, Identities = 107/293 (36%), Positives = 166/293 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  +S    LSRS+A  +I+   V VNG+   K      +  +++  +   VEE   +    +DI  EIV++D+ + +VNKP  ++VHP++   S TL N +  ++  K +      LR GIVHR+DK T GL+++AK+ D+         D+K  +KY A++H +L      ++API R E   R++ +     KEA T F+ + ++ ++TL E+ L TGRTHQIRVH  +I + V  D  YGP+   KT K +GQ+L A  L F HP T + V    + P  F+E+ KK+ +
  S:    11 RLDKALSDLTDLSRSVANEQIKAGQVLVNGQ--PKKAKYSVQVGDVLTYQIPEVEEIDYVA---EDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL--LYHVKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKEAVTRFQVLERFGDYTLVELTLETGRTHQIRVHMAYIGHPVAGDEAYGPR---KTLKGHGQFLHARTLGFTHPRTGEVVEFTAEAPAIFQEHWKKWAR 295
>gi|139473995|ref|YP_001128711.1| putative RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo] >gi|134272242|emb|CAM30494.1| putative RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo] (296 aa)
Score = 399, Expect = 5.9e-37, Identities = 106/290 (36%), Positives = 168/290 (57%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII---LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++    LSR  A  +I+  LV VNG+   K      +  ++I   L +E+++E      P    ++I+YED  + I+NKP  ++VHP++   S T+ N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +    T+    +K  +KYLA++H +L      ++API R E   R++ +     KEA T F  + ++ +++L E++L TGRTHQIRVH  +I + V  DP+YGP+     + +GQ+L A  L   HP T KE+   ++ P+ F++ +K
  S:    10 QRLDKALADLSPLSRGQANDQIKQGLVLVNGQ--QKKAKYTVQAGDVICFELPKEEVLEYQAQNIP----LDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKTDAAHQVLTEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKD-RKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR--KTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLK 291
>gi|21910093|ref|NP_664361.1| putative ribosomal large subunit pseudouridine synthase [Streptococcus pyogenes MGAS315] >gi|28896209|ref|NP_802559.1| hypothetical protein SPs1297 [Streptococcus pyogenes SSI-1] >gi|71903284|ref|YP_280087.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS6180] >gi|94994123|ref|YP_602221.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS10750] >gi|21904284|gb|AAM79164.1| putative ribosomal large subunit pseudouridine synthase [Streptococcus pyogenes MGAS315] >gi|28811460|dbj|BAC64392.1| conserved hypothetical protein [Streptococcus pyogenes SSI-1] >gi|71802379|gb|AAX71732.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS6180] >gi|94547631|gb|ABF37677.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS10750] (296 aa)
Score = 398, Expect = 6.5e-37, Identities = 106/290 (36%), Positives = 168/290 (57%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII---LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++    LSR  A  +I+  LV VNG+   K      +  ++I   L +E+++E      P    ++I+YED  + I+NKP  ++VHP++   S T+ N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +  A  +    +K  +KYLA++H +L      ++API R E   R++ +     KEA T F  + ++ +++L E++L TGRTHQIRVH  +I + V  DP+YGP+     + +GQ+L A  L   HP T KE+   ++ P+ F++ +K
  S:    10 QRLDKALADLSPLSRGQANDQIKQGLVLVNGQ--QKKAKYTVQAGDVICFELPKEEVLEYQAQNIP----LDIIYEDDTLAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKD-RKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR--KTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLK 291
>gi|15674865|ref|NP_269039.1| hypothetical protein SPy_0827 [Streptococcus pyogenes M1 GAS] >gi|50914002|ref|YP_059974.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS10394] >gi|71910451|ref|YP_282001.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS5005] >gi|94988324|ref|YP_596425.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS9429] >gi|13622001|gb|AAK33760.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS] >gi|50903076|gb|AAT86791.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS10394] >gi|71853233|gb|AAZ51256.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS5005] >gi|94541832|gb|ABF31881.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS9429] (296 aa)
Score = 398, Expect = 6.7e-37, Identities = 106/290 (36%), Positives = 168/290 (57%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII---LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++    LSR  A  +I+  LV VNG+   K      +  ++I   L +E+++E      P    ++I+YED  + I+NKP  ++VHP++   S T+ N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +  A  +    +K  +KYLA++H +L      ++API R E   R++ +     KEA T F  + ++ +++L E++L TGRTHQIRVH  +I + V  DP+YGP+     + +GQ+L A  L   HP T KE+   ++ P+ F++ +K
  S:    10 QRLDKALADLSPLSRGQANDQIKQGLVLVNGQ--QKKAKYTVQAGDVICFELPKEEVLEYQAQNIP----LDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKD-RKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR--KTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLK 291
>gi|157150916|ref|YP_001450379.1| RluA family pseudouridine synthase [Streptococcus gordonii str. Challis substr. CH1] >gi|157075710|gb|ABV10393.1| pseudouridine synthase, RluA family [Streptococcus gordonii str. Challis substr. CH1] (296 aa)
Score = 398, Expect = 7.7e-37, Identities = 111/290 (38%), Positives = 170/290 (58%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  V+    LSRS+A  +I+   + VNG ++ K    V +E ++I  E   +EE + +T     +EIVY+D+ + +VNKP  ++VHP++   S TL N + Y I D   I  NG  LR GIVHR+DK T GL+++AK+  +  A      D+K  +KY A++H +L      ++API R E   R++ +     K A T F+ + ++ +++L E++L TGRTHQIRVH  +I + V  D +YGP+   KT K +GQ+L A  L F HP T + +     +P  F+E +KK
  S:    11 RLDKAVADLTDLSRSLANEQIKTGKILVNG-LVKKAKYTV-KEGDVISYELPEIEEIEYVTE-NIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGI--NG-VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR---KTLKGHGQFLHARTLGFTHPRTGEVLEFTAGVPAIFQETLKK 292
>gi|55822493|ref|YP_140934.1| ribosomal large subunit pseudouridine synthase D [Streptococcus thermophilus CNRZ1066] >gi|55738478|gb|AAV62119.1| ribosomal large subunit pseudouridine synthase D [Streptococcus thermophilus CNRZ1066] (292 aa)
Score = 395, Expect = 1.7e-36, Identities = 108/281 (38%), Positives = 160/281 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII---LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMP 286
           RLD  ++    LSRS A   I+   V VNGK  S     V +E ++I   L EE+++E      P    ++I+YED  + +VNKP  ++VHP++   S TL N + Y    K +      +R GIVHR+DK T GL+++AK+  + NA      D+K  +KY+A++H +L      ++API R +   R++ +     K A T F  + ++ N+TL E++L TGRTHQIRVH  +I + V  DP+YGP+   KT K +GQ+L A  L F HP T K V +    P
  S:    11 RLDKSLADLTELSRSQANEAIKAGTVLVNGK--SAKAKYVVKEGDVITYVLPEEEVLEYKAEDIP----LDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMY--HVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD-RKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR---KTLKGHGQFLHAKTLGFTHPTTGKLVELTQKNP 283
>gi|187605859|ref|ZP_02992043.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b] >gi|187482076|gb|EDU20096.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b] (303 aa)
Score = 393, Expect = 2.7e-36, Identities = 108/293 (36%), Positives = 161/293 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           R+D  VS +   SRS  +  I+   + VNG  + K N K+    E+ +   + VE  +VL P    +EIV+ED+ +++VNK   ++VHP +   S TL N + Y  D      NG   R GIVHR+DK T GL++VAK+  +  +      D+ I+++Y+AL+H  L      ++API R     +R    D +AKEA T F+ + +YK+FTL E +L TGRTHQIRVH  +I + +  DP YGP+        GQ L A  L F HP T++ +     +P++F   + K  K
  S:    13 RIDKWVSDRGEWSRSQVQEWIKTGALLVNGSAV-KANYKLQVGDEVEVNVPEAVE-LEVL-PEDIPLEIVFEDEDVIVVNKARGMVVHPAAGHTSGTLVNALLYHCDDLS-GINGVK-RPGIVHRIDKDTTGLLMVAKNDLAHESLASQLKDKTIKREYIALVHGELVHELGTIEAPIGRDTNDRQRMTVTDRNAKEAVTHFRLLERYKDFTLVECKLETGRTHQIRVHMRYIGHPLAGDPKYGPRRTIDLG--GQALHAATLGFHHPRTKEWMEFEAPLPEDFNAELAKLDK 298
>gi|94990203|ref|YP_598303.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS10270] >gi|94543711|gb|ABF33759.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS10270] (296 aa)
Score = 391, Expect = 4.5e-36, Identities = 105/290 (36%), Positives = 167/290 (57%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII---LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++    LSR  A  +I+  LV VN +   K      +  ++I   L +E+++E      P    ++I+YED  + I+NKP  ++VHP++   S T+ N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +  A  +    +K  +KYLA++H +L      ++API R E   R++ +     KEA T F  + ++ +++L E++L TGRTHQIRVH  +I + V  DP+YGP+     + +GQ+L A  L   HP T KE+   ++ P+ F++ +K
  S:    10 QRLDKALADLSPLSRGQANDQIKQGLVLVNDQ--QKKAKYTVQAGDVICFELPKEEVLEYQAQNIP----LDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKD-RKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR--KTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLK 291
>gi|89098727|ref|ZP_01171609.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp. NRRL B-14911] >gi|89086689|gb|EAR65808.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp. NRRL B-14911] (301 aa)
Score = 391, Expect = 4.8e-36, Identities = 116/294 (39%), Positives = 170/294 (57%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTK--VDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           +RLD  VS     LSRS A+  I++  + VNG+  +K N K  +D++ EI   E    EE  VL P + D++I YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  LR GIVHR+DK T GL++VAK+  +  +     +++ + +KY A++H  +      VDAP+ R +   R+ ++     K A T F  I++YK+FT  E +L TGRTHQIRVH ++I   +  DP YGP+   KT +  GQ L A  L F+HP T + +     +P  F E ++K GK
  S:    15 ERLDKAVSLLNEELSRSQAQQMIKDGHILVNGQG-TKTNYKCSIDDKIEISFPEP---EELDVL-PEEMDLDIYYEDGDVLVVNKPKGMVVHPAPGHASGTLVNGLMAHCKDLSGI--NG-VLRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRKYQAIVHGTIPHDYGTVDAPLGR-DPKDRQSMTVVDGGKHAVTHFHVIHRYKDFTHVECQLETGRTHQIRVHMKYIGYPLAGDPKYGPR---KTLEIGGQALHAGVLGFVHPRTGEYMEFEAPLPAYFSELLEKLGK 301
>gi|57866712|ref|YP_188346.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus epidermidis RP62A] >gi|57637370|gb|AAW54158.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Staphylococcus epidermidis RP62A] (305 aa)
Score = 391, Expect = 5.0e-36, Identities = 113/289 (39%), Positives = 171/289 (59%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QR+D LVS      SRS  +  I+  LV VNGK+I K N KV    +I++ E+++VE    + P   +++I YED+ + IV KP  ++VHP+    S TL N + Y I D   I  NG+ +R GIVHR+DK T GL++VAK+  +     +  + + +++KY AL+H ++      +DAPI R   + R+ ++   D KEA T F  +  +K++TL E +L TGRTHQIRVH ++I   ++ DP YGPK   KT    GQ L A  + F HP T K +  +  +P +F++ +
  S:    16 QRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVI-KSNYKVKLNDKIVVTEKEVVEAD--IKPENLNLDIYYEDEDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDLSGI--NGE-IRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSKTVKRKYTALVHGNIPHDYGTIDAPIGR-NKNDRQAMAVVDDGKEAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPK---KTLDIGGQALHAGIIGFEHPVTHKYIEKHATLPNDFEKLL 297
>gi|167217842|ref|ZP_02287478.1| ribosomal large subunit pseudouridine synthase, RluD subfamily protein [Listeria monocytogenes FSL J1-175] (294 aa)
Score = 388, Expect = 9.0e-36, Identities = 104/275 (37%), Positives = 165/275 (60%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEV 279
           +R+D +++     SRS  +  ++N  +TVNG++ +KPN KV    EI   E +  EE +VL    +DI  +I +EDK +L+VNKP  ++VHP++   S TL N +  +F    +      +R GIVHR+DK T GL++VAK+  +  +  K   D+  +++Y+AL+H  +  +   ++API R +   R++++   D KEART F+ + +   +TL   +L TGRTHQIRVH ++I + +  DP YGPK  N     GQ+L A KL F HP T++ +
  S:    15 ERVDKVIAEMMGKSRSAIQLMLKNGDITVNGEL-AKPNYKVQVGDEIHY-EVREPEELEVLA---EDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNAL--LFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKED-RQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK--NTIKGNGQFLHAAKLGFDHPTTKERM 281
>gi|184155639|ref|YP_001843979.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956] >gi|183226983|dbj|BAG27499.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956] (304 aa)
Score = 388, Expect = 9.7e-36, Identities = 101/290 (34%), Positives = 162/290 (55%)
  Q:     4 TQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           T R+D  +   F   SRS  K  I++  VTVNG+ + K   ++     ++++ E  VE    L P    ++IVYED  +L+VNKP  ++VHP     ++TL N + Y      I  NG+ LR GIVHR+DK T GL++VAK+  +  + T    ++   ++Y+AL+H  ++     +DAP+ R     R++ +  +  + A T F+ + +Y+++TL    L TGRTHQIRVH ++I + +  DP+YGP+       +GQYL A  L F HP T +E+      P  F++ +
  S:    15 TGRIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTV-KAKYQLQAGDRVVIEPETPVEID--LEPENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYHAPLSSI--NGE-LRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKENEGTIDAPLAR-SPKDRKKQAVVVGGRHAVTHFRVLKRYQHYTLVACRLETGRTHQIRVHMKYINHPLAGDPLYGPR--KTLPGHGQYLHARLLGFEHPVTGEEMVFTAPWPDYFEQML 296
>gi|160914264|ref|ZP_02076485.1| hypothetical protein EUBDOL_00274 [Eubacterium dolichum DSM 3991] >gi|158433891|gb|EDP12180.1| hypothetical protein EUBDOL_00274 [Eubacterium dolichum DSM 3991] (303 aa)
Score = 388, Expect = 9.7e-36, Identities = 99/293 (33%), Positives = 165/293 (56%)
  Q:     3 NTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           ++QR+D  +S     LSRS     IE   + VNG++I +K   K  +      ++E  +E      P K +++I YED  ++++NKP  I+VHP + + S TL N +  ++  K +      LR GIVHR+DK T GL+IVAK+  +  + +K   ++ + + Y AL+H  ++     +DAPI R     ++      ++K ART F+ + ++  +TL E  L TGRTHQIRVH ++I + V+ D  Y  +   KT   GQ L A++L F+HP T + + +   +PK+F + +++
  S:    13 DSQRIDKYLSMVVEDLSRSRIASLIEEGSILVNGEVIRAKYKVKPADHITAAFEDEMALEAA----PEKMELDIRYEDHDVIVINKPKGIVVHPANGNQSGTLVNGL--LYHCKDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHASLSKQLQNKSVNRLYYALVHGVIEHEFGTIDAPIGRDPKDRQKMAVIATNSKPARTHFRVVERFAKYTLVECRLETGRTHQIRVHMQYIGHPVVGDEKYSYRKTMKTN--GQLLHAHQLTFLHPTTNERITVEAPLPKQFADILEE 299
>gi|31364860|gb|AAP49462.1| YlyB [Streptococcus suis] (297 aa)
Score = 388, Expect = 9.9e-36, Identities = 107/293 (36%), Positives = 165/293 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  +S    LSRS+A  +I+   V VNG+   K      +  +++  +   VEE   +    +DI  EIV++D+ + +VNKP  ++VHP++   S TL N +  ++  K +      LR GIVHR+DK T GL+++AK+ D+         D+K  +KY A++H +L      ++API R E   R++ +     KEA T F+ + ++ ++TL E+ L TGRTHQIRVH  +I + V  D  YGP+   KT K +GQ+L A  L F HP T + V    + P  F+E ++K  K
  S:    11 RLDKALSDLTDLSRSVANEQIKAGQVLVNGQ--PKKAKYSVQVGDVLTYQIPEVEEIDYVA---EDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL--LYHVKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKEAVTRFQVLERFGDYTLVELTLETGRTHQIRVHMAYIGHPVAGDEAYGPR---KTLKGHGQFLHARTLGFTHPRTGEVVEFTAEAPAIFQEALEKLRK 295
>gi|172057958|ref|YP_001814418.1| RluA family pseudouridine synthase [Exiguobacterium sibiricum 255-15] >gi|171990479|gb|ACB61401.1| pseudouridine synthase, RluA family [Exiguobacterium sibiricum 255-15] (307 aa)
Score = 387, Expect = 1.4e-35, Identities = 103/295 (34%), Positives = 167/295 (56%)
  Q:     4 TQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           T R+D  ++ +   SRS  +  ++   V V+G+I+ KPN K+    EI+++  + VE  +VL P    +++VYED  ++++NKP  ++VHP +  +S TL N ++ +  D   I  NG   R GIVHR+DK T GL++VAK+  +  +  +   D+  E+ Y+AL+H  +      ++AP+ R +   +R    D ++K A T F+ + +Y+ FT+ E +L TGRTHQIRVH  +I   +  DP YGP+   K    GQ L A  L F HP T + ++    +P+E    I +  K
  S:    15 TGRIDKWLAEQQDWSRSQVQDWLKAGHVEVDGRIV-KPNYKMSGTEEILVRIPEAVE-LEVL-PEDIPLDVVYEDSDVIVINKPKGMVVHPAAGHVSGTLVNALLHHCQDLSGI--NGVK-RPGIVHRIDKDTSGLLMVAKNDLAHESLAQQLKDKTTERLYIALVHGEIPHELGTIEAPVGRDKNDRQRMTVTDKNSKAAVTHFRVLERYEGFTVVECKLETGRTHQIRVHMRYIGFPLAGDPKYGPRKTMKMN--GQALHAAVLGFKHPRTGEMLHFEAPLPEEMTFEISQLKK 302
>gi|20807974|ref|NP_623145.1| pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter tengcongensis MB4] >gi|20516547|gb|AAM24749.1| Pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter tengcongensis MB4] (309 aa)
Score = 387, Expect = 1.5e-35, Identities = 102/290 (35%), Positives = 167/290 (57%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII--LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D+ ++S+   SRS  K  IE  LV VNGK + KP+ KV E+ E+I  +KE + +E    + P    ++I+YED+ I+++NKP  ++VHP   + S TL N +  ++  K +      LR GIVHRLDK T G+++VAK+  +  + +    ++ + KKY+A++   ++    +++API R     R+ ++   D + A T++K + ++KN T  E  + TGRTHQIRVH  +I + V+ DP+YG K   K    GQ L +  L FIHP     +     +P  F   ++
  S:    18 KRIDVFLASELDYSRSYIKKLIEEGLVLVNGKNV-KPSYKVKEDDEVIVNIKEAEKIE----VVPENIPLDILYEDEDIIVINKPQGMVVHPAPGNYSGTLVNAL--LYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIKERSVLKKYVAIVEGVIKEEEGKIEAPIGR-HPVDRKRMAVVQDGRYALTLYKVLERFKNNTFVEATIKTGRTHQIRVHLSYIGHPVVGDPVYGYKK-QKFKLEGQALHSKVLGFIHPTKGVYMEFEAPLPDYFTRLLE 300
>gi|24379309|ref|NP_721264.1| putative pseudouridylate synthase [Streptococcus mutans UA159] >gi|24377230|gb|AAN58570.1|AE014926_13 putative pseudouridylate synthase [Streptococcus mutans UA159] (296 aa)
Score = 385, Expect = 2.2e-35, Identities = 107/288 (37%), Positives = 159/288 (55%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD  ++    LSRS A  +I+  LV VNGK   K    V E    I+  E+  EE          +EIVYED+ + ++NKP  ++VHP+    S TL N +  +F  K +      +R GIVHR+DK T GL+++AK+  +  A  K   ++K  ++Y+AL+H +L      ++API R E   R++ +     K A T FK + ++  ++L E+ L TGRTHQIRVH  +I + V  DP+Y PK   KT K  GQ+L A  L F HP T + +    ++P  F+E +
  S:    11 RLDKALADLTDLSRSQASEQIKAGLVLVNGKT-QKAKYAVKEGD--IIHYERPQEEVLDCVAQNIPLEIVYEDEDVAVINKPQGMVVHPSVGHPSGTLVNAL--LFHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDQAHQALAKELKEKKSLRQYIALVHGNLPNDRGVIEAPIGRSEKD-RKKQTVTAKGKPAVTHFKVLERFGQYSLVELTLETGRTHQIRVHMAYIGHPVAGDPLYAPK---KTLKGQGQFLHAKTLGFTHPKTGELMQFTTEVPVIFQEVL 290
>gi|51892381|ref|YP_075072.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM 14863] >gi|51856070|dbj|BAD40228.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM 14863] (304 aa)
Score = 384, Expect = 3.0e-35, Identities = 98/290 (33%), Positives = 158/290 (54%)
  Q:     6 RLDILVSSK--FSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK--HINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           R+D+ ++ +    LSRS  +  I+   VT+NG +  K    V+    I+++      E   L P    ++IVYED+ IL+VNK   ++VHP +   + TL + ++  + D + I   G  LR GIVHRLDK T GL++VAKS  +  +  +   D  +++ Y AL+H +    T  ++API R     +R        ++A T F+ + +Y+ + L E  L TGRTHQIRVH  FI + V+ DP+YGP+  H+       Q L A +L F HP + + +   +D P +    +++
  S:    14 RIDVFLAGRPEIGLSRSRIQALIDEGQVTLNGAM-PKARQAVNPGDVIVVRVPD--PEPMELVPEDIPLDIVYEDEDILVVNKQRGLVVHPAAGHWTGTLVHALLDKVDDLEGI---GGELRPGIVHRLDKDTTGLLVVAKSERAMASLQEQIRDHMVQRVYWALVHGNSMPDTGRIEAPIGRHPRDRKRMAVNPKTGRDAVTYFRVLERYRGYALLECRLETGRTHQIRVHLSFIGHPVVGDPLYGPRKPHLGMPP---QALHARQLSFRHPASGEWMEFTVDPPADMMAVVQR 299
>gi|27467790|ref|NP_764427.1| hypothetical protein SE0872 [Staphylococcus epidermidis ATCC 12228] >gi|27315334|gb|AAO04469.1|AE016746_259 conserved hypothetical protein [Staphylococcus epidermidis ATCC 12228] (305 aa)
Score = 384, Expect = 3.2e-35, Identities = 111/289 (38%), Positives = 171/289 (59%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QR+D LVS      SRS  +  I+  LV VNGK+I K N KV    +I++ E+++VE    + P   +++I YED+ + +V KP  ++VHP+    S TL N + Y I D   I  NG+ +R GIVHR+DK T GL++VAK+  +     +  + + +++KY AL+H ++      +DAPI R   + R+ ++   D KEA T F  +  +K++TL E +L TGRTHQIRVH ++I   ++ DP YGPK   KT    GQ L A  + F HP T + +  +  +P +F++ +
  S:    16 QRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVI-KSNYKVKLNDKIVVTEKEVVEAD--IKPENLNLDIYYEDEDVAVVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDLSGI--NGE-IRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSKTVKRKYTALVHGNIPHDYGTIDAPIGR-NKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPK---KTLDIDGQALHAGIIGFEHPVTHEYIEKHATLPNDFEKLL 297
>gi|148544158|ref|YP_001271528.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus reuteri F275] >gi|184153530|ref|YP_001841871.1| pseudouridylate synthase [Lactobacillus reuteri F275] >gi|148531192|gb|ABQ83191.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus reuteri F275] >gi|183224874|dbj|BAG25391.1| pseudouridylate synthase [Lactobacillus reuteri F275] (303 aa)
Score = 384, Expect = 3.2e-35, Identities = 105/293 (35%), Positives = 165/293 (56%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTK--VDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           R+D  +   F   SRS  +H IE+  V VNGK + KP  K  V +  +II +E + ++    L P    ++IVYED  +++VNKP  ++VHP      +TL N +  ++ S     NG+  R GIVHR+DK T GL++VAK+  +  + T     +  +++Y+AL+H  ++     +DAP+ R     R++ +  +D + A T F  + ++KN+TL   +L TGRTHQIRVH ++I + +  DP+YGP+        GQYL A  L F HP T KE+     +P  F + ++   K
  S:    16 RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGKQV-KPKYKLLVGDHVQIIPEEPQKID----LAPEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNAL--LYHSPLSTINGE-FRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPLGR-SLKDRKKQAVVVDGRHAVTHFNVLERFKNYTLVACQLETGRTHQIRVHMKYIGHPLAGDPLYGPR--KTLAGNGQYLHARLLGFKHPRTGKEMVFTAPLPAYFVKMLEHLRK 300
>gi|196162765|ref|ZP_03123296.1| putative pseudouridylate synthase [Clostridium difficile QCD-23m63] (315 aa)
Score = 383, Expect = 3.8e-35, Identities = 114/290 (39%), Positives = 165/290 (56%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVL--TPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLDI ++ +   +SRS  +  I++  V VN KI  K    V EE  I+++    + E KVL   P    I+IVYED  +LI+NKP D++VHP   +  NTL N I Y    K    NG  +R GIVHR+DK T GL+++AK+  + N   +   +  I ++Y  + +  ++   + VD PI R     R +++   D K A T F+ + ++  FT    +L TGRTHQIRVHA  I + ++ D +YGPK      K GQ L A KL FIHP T++ +  N ++P+ FKE IKK
  S:    29 RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKI-EKAKYLVKEEDNIVIE----IPEPKVLEVVPQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSING-VIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKENKITVDKPIGR-NPKDRLKMAVVKDGKNAITHFEVVERFDKFTHMRAKLETGRTHQIRVHALSINHPLLGDYVYGPKETKFKLK-GQTLHAKKLGFIHPTTKEYIEFNSELPEYFKEVIKK 313
>gi|116333479|ref|YP_795006.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis ATCC 367] >gi|116098826|gb|ABJ63975.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus brevis ATCC 367] (307 aa)
Score = 383, Expect = 4.0e-35, Identities = 105/291 (36%), Positives = 166/291 (57%)
  Q:     4 TQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIIS-KPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           T+RLD LV+    ++SRS AK  IE   +TV+G  +  K   KV     + L + + ++    LTP    +EIVYED  +L+VNKP  ++VHP     ++TL N +  ++ S   + NG  LR GIVHR+DK T GL++VAK+  +  + +     +   ++Y+A++H +++     + AP+ R     R++ +   D + A T F+ + +Y  +TL    L TGRTHQIRVH  +I + V  DP+YGPK   KT K  GQ+L A +L F  P T +E+     +P+ F + ++
  S:    11 TERLDKLVADAVATVSRSQAKLAIEAGQITVDGATVKPKDKPKVGATIRVSLPDPEPLD----LTPEDIPLEIVYEDADVLVVNKPQGMVVHPAPGHPNHTLVNAL--LYHSPLSQINGT-LRPGIVHRIDKDTSGLLMVAKNDHAHQSLSAQLQAKTNLREYVAIVHGNIKEEDGVIRAPLGR-SPKDRKKQAIVADGRPAVTHFRVLERYGTYTLIACRLETGRTHQIRVHMAYINHPVAGDPLYGPK---KTLKGAGQFLHARELGFKQPTTGEELVFTAPVPENFAKAVR 293
>gi|70726718|ref|YP_253632.1| hypothetical protein SH1717 [Staphylococcus haemolyticus JCSC1435] >gi|68447442|dbj|BAE05026.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435] (305 aa)
Score = 383, Expect = 4.1e-35, Identities = 112/290 (38%), Positives = 170/290 (58%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QR+D L+       SRS  +  I+ +LVTVN K+I K N KV     II+ E+++VE    + P   +++I YED+ + IV KP  ++VHP+    S TL N + Y I D   I  NG+ +R GIVHR+DK T GL++VAK+  +     +  +D+ +++KY AL+H ++      +DAPI R E   R+ +    + KEA T F  +  + ++TL E +L TGRTHQIRVH ++I   ++ DP YGP+   KT    GQ L A  + F HP T + +    ++PKEF+  ++
  S:    16 QRIDKLLPEFNNEWSRSQIQDLIKEDLVTVNEKVI-KSNYKVKLNDLIIVTEKEVVEAD--IQPENLNLDIYYEDEDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDLSGI--NGE-IRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYTALVHGNIPHDYGTIDAPIGRNEKD-RQSMDVVDNGKEAVTHFNVLEHFNDYTLIECQLETGRTHQIRVHMKYIGFPLVGDPKYGPR---KTLDIGGQALHAGVIGFEHPVTHEYIERQAELPKEFETLLE 298
>gi|118051071|ref|ZP_01519620.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1] >gi|118001742|gb|EAV15897.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1] (358 aa)
Score = 383, Expect = 4.3e-35, Identities = 98/293 (33%), Positives = 165/293 (56%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRT-VEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           QR+D +++   S  SRS  +  + +  VT+NGK++ KP+ KV     + + E +  +++    P   D+++VYED+ +L++NKP  ++VHP   + + TL N +     ++  K    P R GIVHRLDK T GL++VA++  + +A  K+   +++ ++YLAL H    +R   EVDAPI R   +  R    D++    K+ART F  ++     +L    L TGRTHQIRVH   + + +I D +YG +      +  Q L A++L F HP T+K +  +  +P++    +  +G
  S:    54 QRVDKVLALGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRV-EMRPTQQSMAFQPEAMDLQVVYEDEDLLVINKPAGLVVHPAPGNWTGTLLNGLL----ARDEKARQVP-RAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQYLALAHKQWGSRKRREVDAPIGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDGDAAHSLVRCTLHTGRTHQIRVHMASLGHPLIADTLYGGQPEGGLER--QALHAFRLAFEHPVTKKPLVHHAPLPQDMAGALDLWG 343
>gi|194468025|ref|ZP_03074011.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23] >gi|194452878|gb|EDX41776.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23] (303 aa)
Score = 382, Expect = 4.4e-35, Identities = 105/293 (35%), Positives = 164/293 (55%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTK--VDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           R+D  +   F   SRS  +H IE+  V VNGK + KP  K  V +  +II +E + ++    L P    ++IVYED  +++VNKP  ++VHP      +TL N +  ++ S     NG+  R GIVHR+DK T GL++VAK+  +  + T     +  +++Y+AL+H  ++     +DAP+ R     R++    +D + A T F  + ++KN+TL   +L TGRTHQIRVH ++I + +  DP+YGP+        GQYL A  L F HP T KE+     +P  F + ++   K
  S:    16 RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGKQV-KPKYKLLVGDHVQIIPEEPQKID----LAPEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNAL--LYHSPLSTINGE-FRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPLGR-SLKDRKKQGVVVDGRHAVTHFNVLERFKNYTLVACQLETGRTHQIRVHMKYIGHPLAGDPLYGPR--KTLAGNGQYLHARLLGFKHPRTGKEMVFTAPLPAYFVKMLEHLRK 300
>gi|158320450|ref|YP_001512957.1| RluA family pseudouridine synthase [Alkaliphilus oremlandii OhILAs] >gi|158140649|gb|ABW18961.1| pseudouridine synthase, RluA family [Alkaliphilus oremlandii OhILAs] (308 aa)
Score = 382, Expect = 4.6e-35, Identities = 106/289 (36%), Positives = 167/289 (57%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKI-ISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ +S ++  LSRS  +  I+++ + VNGKI  +K   K+ +E EI L +   VEE  +  P    + IVYED+ +++V+KP  ++VHP   + S TL N + +   ++    NG P+R GIVHR+DK T GL++VAK+  +     + F      +KY A++  +++ +   VDAPI R      +    + D K A T FK +  +++FT  E +L TGRTHQIRVH  +I N ++ DP+YG K  +K    GQ L A    FIHP T++ +    D+P+ F + ++
  S:    16 RLDLYISEQYEELSRSYIQKLIKDHHIKVNGKIEKAKYMIKLGDEIEINLPQ---VEEVTI-EPENIPLTIVYEDEDVIVVDKPQGMVVHPAPGNYSGTLVNALLFHCKNQLSDVNG-PMRPGIVHRIDKDTSGLLVVAKNNAAHEILAEQFRAHTNTRKYHAIVVGNIREKEAAVDAPIGRHPVDRLKRAVMN-DGKHAVTHFKVLEVFRDFTYIEAKLETGRTHQIRVHLSYIGNPLVGDPLYGAKS-SKFNLKGQILHAKVFGFIHPKTKEYMEFTSDLPEYFNKVLR 299
>gi|168716044|ref|ZP_02748321.1| putative pseudouridylate synthase [Clostridium difficile QCD-63q42] >gi|196126743|ref|ZP_03118492.1| putative pseudouridylate synthase [Clostridium difficile ATCC 43255] (315 aa)
Score = 382, Expect = 5.7e-35, Identities = 113/290 (38%), Positives = 165/290 (56%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLDI ++ +   +SRS  +  I++  V VN K+  K    V EE  I+++    + E KVL    +DI  +IVYED  +LI+NKP D++VHP   +  NTL N I Y    K    NG  +R GIVHR+DK T GL+++AK+  + N   +   +  I ++Y  + +  ++   + VD PI R     R +++   D K A T F+ + ++  FT     L TGRTHQIRVHA  I + ++ D +YGPK      K GQ L A KL FIHP T++ +  N ++P+ FKE IKK
  S:    29 RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKV-EKARYLVKEEDNIVIE----IPEPKVLEVLPQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSING-VIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGR-NPKDRLKMAVVKDGKNAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLLGDYVYGPKETKFKLK-GQTLHAKKLGFIHPTTKEYIEFNSELPEYFKEVIKK 313
>gi|90961803|ref|YP_535719.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus salivarius UCC118] >gi|90820997|gb|ABD99636.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus salivarius UCC118] (298 aa)
Score = 381, Expect = 6.3e-35, Identities = 100/295 (33%), Positives = 172/295 (58%)
  Q:     4 TQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           T RLD +V++ F+  +RS  K  I++  + VNG +  K N KV+   EI   + ++ + +  L P    ++IVYED  +++VNKP  ++VHP+     +TL N +  ++ S     NG   R GIVHR+DK T GL++VAK+  +  +  K   D+   ++Y+AL+H +++  +  +DAP+ R +   +++     D + A T F+ + +Y ++TL +  L TGRTHQIRVH ++I + ++ D +YGP+     +  GQ+L A KL F+HP T + +     +P+ FK+ ++   K
  S:    11 TGRLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDV-KKANYKVNLGDEITFDKPEVKKLS--LEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNAL--LYHSPLSTINGT-YRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYVALVHGNIKEDSGTIDAPLGRSKVDRKKQAVVK-DGRNAVTHFEVLKRYGDYTLVKCVLETGRTHQIRVHMKYIGHPLVGDQLYGPRKTLGNS--GQFLHAEKLGFVHPRTNEYLEFTAPLPENFKKLLESLDK 297
>gi|126700216|ref|YP_001089113.1| putative pseudouridylate synthase [Clostridium difficile 630] >gi|115251653|emb|CAJ69486.1| putative pseudouridylate synthase [Clostridium difficile 630] (303 aa)
Score = 381, Expect = 6.7e-35, Identities = 113/290 (38%), Positives = 165/290 (56%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLDI ++ +   +SRS  +  I++  V VN K+  K    V EE  I+++    + E KVL    +DI  +IVYED  +LI+NKP D++VHP   +  NTL N I Y    K    NG  +R GIVHR+DK T GL+++AK+  + N   +   +  I ++Y  + +  ++   + VD PI R     R +++   D K A T F+ + ++  FT     L TGRTHQIRVHA  I + ++ D +YGPK      K GQ L A KL FIHP T++ +  N ++P+ FKE IKK
  S:    17 RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKV-EKARYLVKEEDNIVIE----IPEPKVLEVLPQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSING-VIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGR-NPKDRLKMAVVKDGKNAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLLGDYVYGPKETKFKLK-GQTLHAKKLGFIHPTTKEYIEFNSELPEYFKEVIKK 301
>gi|168694220|ref|ZP_02726497.1| putative pseudouridylate synthase [Clostridium difficile QCD-37x79] >gi|168725312|ref|ZP_02757589.1| putative pseudouridylate synthase [Clostridium difficile QCD-76w55] >gi|168732667|ref|ZP_02764944.1| putative pseudouridylate synthase [Clostridium difficile QCD-97b34] >gi|196159237|ref|ZP_03119798.1| putative pseudouridylate synthase [Clostridium difficile CIP 107932] (315 aa)
Score = 381, Expect = 7.0e-35, Identities = 113/290 (38%), Positives = 165/290 (56%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLDI ++ +   +SRS  +  I++  V VN K+  K    V EE  I+++    + E KVL    +DI  +IVYED  +LI+NKP D++VHP   +  NTL N I Y    K    NG  +R GIVHR+DK T GL+++AK+  + N   +   +  I ++Y  + +  ++   + VD PI R     R +++   D K A T F+ + ++  FT     L TGRTHQIRVHA  I + ++ D +YGPK      K GQ L A KL FIHP T++ +  N ++P+ FKE IKK
  S:    29 RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKV-EKAKYLVKEEDNIVIE----IPEPKVLEVLPQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSING-VIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGR-NPKDRLKMAVVKDGKNAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLLGDFVYGPKETKFKLK-GQTLHAKKLGFIHPTTKEYIEFNSELPEYFKEAIKK 313
>gi|168139860|ref|ZP_02583089.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus G9842] (302 aa)
Score = 380, Expect = 8.5e-35, Identities = 107/287 (37%), Positives = 161/287 (56%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +R+D  V+      SRS  +  I++++VTVNGK + K N KV EE EI +       E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F+E
  S:    16 ERIDKFVAGINNEWSRSQVQQWIKDDVVTVNGKAV-KVNYKVKEEDEITVTIPD--PEALDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIGR-DKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIQFEAPIPEVFEE 295
>gi|160900458|ref|YP_001566040.1| RluA family pseudouridine synthase [Delftia acidovorans SPH-1] >gi|160366042|gb|ABX37655.1| pseudouridine synthase, RluA family [Delftia acidovorans SPH-1] (356 aa)
Score = 379, Expect = 1.2e-34, Identities = 94/289 (32%), Positives = 152/289 (52%)
  Q:     9 ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRT-VEVDAPIKRVETSTRREVSRDI---DAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +L       SRS  +  +    VT+NG+++ KP TKV     ++L E +  +++    P    +++VYED+++L+VNKP  ++VHP   + + TL N +      +  K    P R GIVHRLDK T GL++VA+S  + +A   +   + + ++YLAL H     R   EVDAPI R   +  R    D+     K ART    +   +  +L    L TGRTHQIRVH   + + ++ D +YG K      +  Q L A++L F HP T + + +   +P +  + ++ +G
  S:    63 VLAECVAEFSRSYLQQLLAQGAVTLNGRVLVKPATKVAAGDRMVL-EMRPTQQSMAFQPEDMALDVVYEDEHLLVVNKPAGLVVHPAPGNWTGTLLNGLL----GRDPKAREVP-RAGIVHRLDKDTSGLMVVARSRAAMDALVAMIAARDVSRQYLALAHKAWGPRKHREVDAPIGRDPRNRLRMAVVDLAQHAGKTARTDIDLLAGNEEVSLVRCTLHTGRTHQIRVHMASLGHPLVADAVYGGKEAGGMAR--QALHAFRLAFTHPMTGQALVLRAPLPPDMAQALENWG 347
>gi|30021981|ref|NP_833612.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus ATCC 14579] >gi|29897537|gb|AAP10813.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus ATCC 14579] (302 aa)
Score = 378, Expect = 1.5e-34, Identities = 106/290 (36%), Positives = 163/290 (56%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +  +R+D  V+      SR+  +  I++N+VTVNGK + K N KV EE EI +   +   E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F++
  S:    13 QKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAV-KGNYKVKEEDEITVTIPE--PEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIQFEAPIPEVFED 295
>gi|154504404|ref|ZP_02041142.1| hypothetical protein RUMGNA_01908 [Ruminococcus gnavus ATCC 29149] >gi|153795333|gb|EDN77753.1| hypothetical protein RUMGNA_01908 [Ruminococcus gnavus ATCC 29149] (309 aa)
Score = 378, Expect = 1.5e-34, Identities = 101/294 (34%), Positives = 161/294 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           +R+D  +S++    SRS  +  I++ LV VNGK + K N K+  E E+ L+  ++  E   + P +  ++I+YED  +L+VNKP  ++VHP     + TL N + Y         NG  +R GIVHR+D  T G ++V K+  +     +   D  I ++Y A++H +L+  +  V+API R  T  ++        +EA T ++ + ++ N+T  E EL TGRTHQIRVH   I + ++ D +YGP       + GQ L A  L F+HP T   V  +  +P+ F+E +KK  K
  S:    16 ERIDKFLSAQMPDRSRSYIQKLIKDGLVEVNGKQV-KTNYKLGSEDEVKLQIPEL--EVPDILPEEIPLDILYEDTDLLVVNKPKGMVVHPAPGHYTGTLVNALMYHCRENLSGING-VMRPGIVHRIDMDTTGSLLVCKNDRAHQILAEQLKDHSITRRYEAIVHGNLKEDSGTVNAPIGRHPTDRKKMSVHAPHGREAVTHYRVLERFGNYTHIECELETGRTHQIRVHMASIGHPILGDLVYGPTKCPFRLQ-GQTLHARILGFVHPSTGAYVQFDAPLPEYFEELLKKLRK 305
>gi|168162165|ref|ZP_02597398.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus H3081.97] (302 aa)
Score = 377, Expect = 2.0e-34, Identities = 106/290 (36%), Positives = 162/290 (55%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +  +R+D  V+      SR+  +  I++N+VTVNGK + K N KV E  EI +   +   E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T K +     +P+ F++
  S:    13 QKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAV-KGNYKVRENDEITVTIPE--PEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGKYIQFEAPIPEVFED 295
>gi|125973425|ref|YP_001037335.1| ribosomal large subunit pseudouridine synthase D [Clostridium thermocellum ATCC 27405] >gi|196253292|ref|ZP_03151926.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM 4150] >gi|125713650|gb|ABN52142.1| ribosomal large subunit pseudouridine synthase D [Clostridium thermocellum ATCC 27405] >gi|196197307|gb|EDX92170.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM 4150] (303 aa)
Score = 376, Expect = 2.8e-34, Identities = 99/281 (35%), Positives = 160/281 (56%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIE--IVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           SRS  +  I + ++ VNGK + K N K+ +  EI+ +    + E +VL    +DI+  I+YED++I++V+KP  ++VHP + + S TL N +     +     NG  +R GIVHR+DK T G+++VAKS  +    ++   D  IE+ Y+A++H  ++    ++DAPI R     ++      + + A T FK + ++K+ T  E  L TGRTHQIRVH  +I   +I D +YG K+ +     GQ L A KL F+HP   + +     +P+ FKE ++K  K
  S:    27 SRSYIQKLINDGMILVNGKPV-KSNYKIKQNDEILAR----IPEPQVLDVVAEDIDVPILYEDEHIIVVDKPKGMVVHPAAGNYSGTLVNALLKHCGTNLSNING-IIRPGIVHRIDKDTSGVLVVAKSNAAHEGLSEKLKDHDIERVYIAVVHGIIREDYGKIDAPIGRHPVDRKKMAVNTKNGRRAVTRFKVLERFKDATYIEATLETGRTHQIRVHMSYIGFPIIGDTVYGRKN-DIYNINGQALHAKKLGFVHPIKGEYMEFESPLPEYFKELLEKLRK 302
>gi|146296933|ref|YP_001180704.1| RluA family pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM 8903] >gi|145410509|gb|ABP67513.1| ribosomal large subunit pseudouridine synthase D [Caldicellulosiruptor saccharolyticus DSM 8903] (300 aa)
Score = 375, Expect = 3.2e-34, Identities = 101/288 (35%), Positives = 166/288 (57%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD  +S   S +RS  +  IE   V VN   + KP  KV +  +II   + ++ E K L+   +DI  E+VYED+++ ++NKP  ++VHP + +  NTL N + + F  +    NG  +R GIVHRLDK T GL+IVAK+ ++    ++     +I++ Y A+    L+  +  ++API R     R +++   + KEA T F+ + ++  +T  ++ L TGRTHQIRVH  +I   ++ D  YG +  N+    GQ L A +++F+HP T K ++ + D+P+ F E +
  S:     9 RLDKYLSEALSKTRSFVQKIIEEGNVWVNQSQVLKPAYKV-KSGDII---KVVIPEPKQLSLVAQDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKFSGRLSSING-VIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGR-HPVNRLKMAVVPNGKEAVTYFEVLERFDKYTFIKLRLKTGRTHQIRVHMSYIGYPLLGDSSYG-RAKNEFGVQGQVLHAGEIEFVHPITSKVLHFSADLPEYFLEIL 291
>gi|194015066|ref|ZP_03053683.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus pumilus ATCC 7061] >gi|194014092|gb|EDW23657.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus pumilus ATCC 7061] (304 aa)
Score = 375, Expect = 3.6e-34, Identities = 104/292 (35%), Positives = 167/292 (57%)
  Q:     2 KNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKK--DIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           + ++RLD  L +++   SR+  +  +++ L+ VNGK + K N KV    +I ++    + E +VL    +  D++I YED  +L+VNKP  ++VHP    +S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + +KY A++H  +Q  T  +DAPI R +   +        AK+A T F  I ++++FT+ E  L TGRTHQIRVH ++I   +  DP YGP+   KT  + GQ L A  L F HP T + +     +P + + +I
  S:    12 QTSERLDKFLSTTEPEWSRTQVQQWVKDGLIEVNGKQV-KANYKVQAGDQIKVE----IPEPEVLDVEAEPMDLDIYYEDADVLVVNKPRGMVVHPAPGHVSGTLVNGLMAHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKYTAVVHGIIQHDTGTIDAPIGRDKKDRQSMTVTKESAKQAVTHFDVIERFQDFTVVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPR---KTVDFNGQLLHAGVLGFDHPRTGEYIEFTAPIPADMQAFI 297
>gi|149019517|ref|ZP_01834836.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP23-BS72] >gi|147930892|gb|EDK81872.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pneumoniae SP23-BS72] (237 aa)
Score = 374, Expect = 4.5e-34, Identities = 93/227 (40%), Positives = 140/227 (61%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           +EIVY+D+ + +VNKP  ++VHP++   S TL N + Y I D   I  NG  LR GIVHR+DK T GL+++AK+ D+  A  +   D+K  +KY A++H +L      ++API R E   R++ +     K A T F  + ++ +++L E++L TGRTHQIRVH  +I + V  D +YGP+   KT K +GQ+L A  L F HP T K +    D+P+ FKE +++  K
  S:    16 LEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGI--NG-VLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD-RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSVAGDEVYGPR---KTLKGHGQFLHAKTLGFTHPRTGKTLEFKADIPEIFKETLERLRK 237
>gi|134299530|ref|YP_001113026.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1] >gi|134052230|gb|ABO50201.1| ribosomal large subunit pseudouridine synthase D [Desulfotomaculum reducens MI-1] (306 aa)
Score = 374, Expect = 4.6e-34, Identities = 102/290 (35%), Positives = 167/290 (57%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK----HINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD+ ++++   +SRS  +  IE+ LVTV+GK  ++ N K+  E E I  +    EE KV  P    ++I YED ++++VNKP  ++VHP   +++ TL N + Y   D   I  NG  +R GIVHRLDK T GL++ AK   +  +  +   D+ + ++Y AL+H++++     ++API R     ++    + ++K A T F+ + ++ ++TL E  L TGRTHQIRVH  +I   ++ DP YGP     H++     GQ L A  L F+HP + + +     +P  F+  + K
  S:    16 RLDVFLANQCQDISRSYIQKLIEDGLVTVDGKP-ARANHKLRVE-ETIHMQIPPAEELKV-EPENIPLDIYYEDSHVIVVNKPRGMVVHPAEGNIAGTLVNALLYHCHDLSGI--NG-IMRPGIVHRLDKDTSGLIMAAKHDQAHQSLARQLKDRTVTRRYQALVHHNIKGDFGTINAPIGRDPRDRQKMAVVERNSKNAVTHFQVLERFGDYTLIECRLETGRTHQIRVHMAYIGFPLVGDPKYGPSKSHFHLD-----GQLLHAKVLGFLHPVSGEYLEFIAPLPDVFENVLVK 300
>gi|87161600|ref|YP_493787.1| hypothetical protein SAUSA300_1090 [Staphylococcus aureus subsp. aureus USA300] >gi|161509370|ref|YP_001575029.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus USA300_TCH1516] >gi|168729554|ref|ZP_02761831.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus USA300_TCH1516] >gi|87127574|gb|ABD22088.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus USA300_FPR3757] >gi|160368179|gb|ABX29150.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus USA300_TCH1516] (305 aa)
Score = 374, Expect = 4.6e-34, Identities = 97/276 (35%), Positives = 160/276 (57%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           SR+  +  I+  LV  N K++ K N KV     I++ E+++VE    + P   +++I YED  + +V KP  ++VHP+    +NTL N + Y    K +      +R GIVHR+D  T GL++VAK+  +     +  +D+ +++KY+AL+H ++      +DAPI R   + R+ ++   D KEA T F  +  +K++TL E +L TGRTHQIRVH ++I   ++ DP YGPK   KT    GQ L A  + F HP T + +  + ++P++F++ +
  S:    30 SRNQIQDWIKAGLVVANDKVV-KSNYKVKLNDHIVVTEKEVVEAD--ILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMY--QIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGR-NKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPK---KTLDIGGQALHAGLIGFEHPVTSEYIERHAELPQDFEDLL 297
>gi|15924187|ref|NP_371721.1| ribosomal large subunit psudouridine synthase D [Staphylococcus aureus subsp. aureus Mu50] >gi|15926780|ref|NP_374313.1| hypothetical protein SA1040 [Staphylococcus aureus subsp. aureus N315] >gi|57651766|ref|YP_186072.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus aureus subsp. aureus COL] >gi|88194903|ref|YP_499703.1| hypothetical protein SAOUHSC_01163 [Staphylococcus aureus subsp. aureus NCTC 8325] >gi|148267688|ref|YP_001246631.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp. aureus JH9] >gi|150393746|ref|YP_001316421.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1] >gi|151221320|ref|YP_001332142.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str. Newman] >gi|156979518|ref|YP_001441777.1| hypothetical protein SAHV_1187 [Staphylococcus aureus subsp. aureus Mu3] >gi|13700996|dbj|BAB42292.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus N315] >gi|14246967|dbj|BAB57359.1| similar to ribosomal large subunit psudouridine synthase D [Staphylococcus aureus subsp. aureus Mu50] >gi|57285952|gb|AAW38046.1| ribosomal large subunit pseudouridine synthases, RluD subfamily [Staphylococcus aureus subsp. aureus COL] >gi|87202461|gb|ABD30271.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus NCTC 8325] >gi|147740757|gb|ABQ49055.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus aureus subsp. aureus JH9] >gi|149946198|gb|ABR52134.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp. aureus JH1] >gi|150374120|dbj|BAF67380.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str. Newman] >gi|156721653|dbj|BAF78070.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus Mu3] (305 aa)
Score = 373, Expect = 5.4e-34, Identities = 97/276 (35%), Positives = 160/276 (57%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           SR+  +  I+  LV  N K++ K N KV     I++ E+++VE    + P   +++I YED  + +V KP  ++VHP+    +NTL N + Y    K +      +R GIVHR+D  T GL++VAK+  +     +  +D+ +++KY+AL+H ++      +DAPI R   + R+ ++   D KEA T F  +  +K++TL E +L TGRTHQIRVH ++I   ++ DP YGPK   KT    GQ L A  + F HP T + +  + ++P++F++ +
  S:    30 SRNQIQDWIKAGLVVANDKVV-KSNYKVKLNDHIVVTEKEVVEAD--ILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMY--QIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGR-NKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPK---KTLDIGGQALHAGLIGFEHPVTGEYIERHAELPQDFEDLL 297
>gi|1373157|gb|AAB57767.1| orf-X; hypothetical protein; Method: conceptual translation supplied by author (303 aa)
Score = 373, Expect = 5.7e-34, Identities = 103/297 (34%), Positives = 168/297 (56%)
  Q:     2 KNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKK--DIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           + ++R+D  L S++   SR+  +  +++  V VNG  + K N K+    ++ +     V E + L    +  D++I YED+ +L+VNKP  ++VHP    L+ TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     +++ + +KY A++H  +      +DAPI R +   R+ ++   D K A T F  + ++++FTL E +L TGRTHQIRVH ++I   +  DP YGP+   KT  + GQ L A  L F HP T + V     +P++  E I+   K
  S:    12 QKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAV-KANYKIQPGDQVTVT----VPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLISHDDGTIDAPIGR-DKKDRQSMTVTRDGKNAVTHFHVLERFQDFTLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPR---KTIDFNGQALHAGVLGFDHPRTGEYVEFEAPLPEDMAELIENLRK 301
>gi|157692226|ref|YP_001486688.1| pseudouridylate synthase [Bacillus pumilus SAFR-032] >gi|157680984|gb|ABV62128.1| pseudouridylate synthase [Bacillus pumilus SAFR-032] (304 aa)
Score = 373, Expect = 6.2e-34, Identities = 104/292 (35%), Positives = 165/292 (56%)
  Q:     2 KNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEI---ILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           + ++RLD  L +S+   SR+  +  +++ L+ VNGK + K N KV    +I   I + E +  E + +     D++I YED  +L+VNKP  ++VHP    +S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + +KY A++H  +Q  T  +DAPI R +   +        +K+A T F  I ++ +FT+ E  L TGRTHQIRVH ++I   +  DP YGP+   KT  + GQ L A  L F HP T + +     +P + + +I
  S:    12 QTSERLDKFLSTSEPEWSRTQVQQWVKDGLIEVNGKQV-KANYKVQAGDQIKVEIPEPEALDVEAEAM-----DLDIYYEDADVLVVNKPRGMVVHPAPGHVSGTLVNGLMAHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKYTAVVHGIIQHDTGTIDAPIGRDKKDRQSMTVTKESSKQAVTHFDVIERFDDFTVVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPR---KTVDFNGQLLHAGVLGFDHPRTGEYIEFTAPVPADMRGFI 297
>gi|116492705|ref|YP_804440.1| ribosomal large subunit pseudouridine synthase D [Pediococcus pentosaceus ATCC 25745] >gi|116102855|gb|ABJ67998.1| ribosomal large subunit pseudouridine synthase D [Pediococcus pentosaceus ATCC 25745] (300 aa)
Score = 372, Expect = 7.4e-34, Identities = 102/294 (34%), Positives = 168/294 (57%)
  Q:     2 KNTQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNT---KVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + + RLD +V++ +  L+RS  ++ I+   + VN      P T   KV E   I +     VE +  + P K +++IV+ED  +++VNKP  ++VHP     + TL N    + D   +      LR GIVHR+DK T GL++VAK+  +  + +     +  ++KYLA++H + +     ++API R +   R++++   D + A T FK + ++ ++TL E EL TGRTHQIRVH ++I + V  DP+YGP+  N     GQ+L A  L F HP T +E+   +D P+ F++ + K
  S:    11 QESGRLDKVVTNHYPDLTRSKIQNLIKQEQILVN----QAPTTNRYKVSENDVIDVTLPDPVEVS--VKPEKMNLDIVFEDDDVIVVNKPQGMVVHPAPGHENGTLVN---GLLDHAPLATVNGELRPGIVHRIDKDTSGLLMVAKNDQAMLSLSAQLKAKTNQRKYLAIVHGNFKEEAGTINAPIGRSKKD-RKKMAIVEDGRPAVTHFKVLERFTDYTLIECELETGRTHQIRVHLKYIGHPVAGDPLYGPR--NTLKGNGQFLHAKLLGFKHPRTGEELVFEVDPPQIFQDTLSK 296
>gi|168136872|ref|ZP_02580101.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus B4264] (302 aa)
Score = 372, Expect = 7.9e-34, Identities = 105/290 (36%), Positives = 162/290 (55%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +  +R+D  V+      SR+  +  I++ +VTVNGK + K N KV EE EI +   +   E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F++
  S:    13 QKNERIDKFVTGINNEWSRTQVQQWIKDEVVTVNGKAV-KGNYKVKEEDEITVTIPE--PEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIQFEAPIPEVFED 295
>gi|89895611|ref|YP_519098.1| hypothetical protein DSY2865 [Desulfitobacterium hafniense Y51] >gi|89335059|dbj|BAE84654.1| hypothetical protein [Desulfitobacterium hafniense Y51] (300 aa)
Score = 371, Expect = 8.6e-34, Identities = 95/268 (35%), Positives = 148/268 (55%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIIL-----KEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHP 273
           RLD+ V+ +   SRS  +  IE   + VNG    K N KV    +I +     +E K+  E   L       E++YED+ +L+VNKP  ++VHP     + T+ N +  ++  + +      LR GIVHR+DK T GL++VAK+  +     +      + ++YLA++H  +   +  VDAP+ R     ++      +AKEA T ++ + ++++FTL E  L TGRTHQIRVH  ++K+ V+ DP+YGP+  N     GQ L A  L F HP
  S:    10 RLDVGVTERVGKSRSFIQGLIEEGHILVNGAA-RKANYKVRAMDQITVVIPPPRELKVEAENIPL-------EVLYEDEDVLVVNKPQGMVVHPAPGAWTKTMVNAL--LYHCRNLSGINGVLRPGIVHRIDKDTSGLLVVAKNDLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTVDAPVGRDPADRKKMAVVFQNAKEAVTHYEVLERFRDFTLLEARLETGRTHQIRVHMAYLKHPVLGDPLYGPRK-NPFGLQGQMLHAQLLGFQHP 271
>gi|152976253|ref|YP_001375770.1| RluA family pseudouridine synthase [Bacillus cereus subsp. cytotoxis NVH 391-98] >gi|152025005|gb|ABS22775.1| pseudouridine synthase, RluA family [Bacillus cereus subsp. cytotoxis NVH 391-98] (302 aa)
Score = 371, Expect = 9.3e-34, Identities = 110/290 (37%), Positives = 163/290 (56%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKD--IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +  +R+D  V+S     SR+  +  I++ ++TVNGK + K N KV E  EI +     V E + L    +D  +EI YED  +L+VNKP  ++VHP     S TL N + Y   D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     +++ + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK   KT    GQ L A  L F HP T + +      P  F+E
  S:    13 RKNERIDKFVASVNHEWSRTQVQQWIKDGVITVNGKTV-KGNYKVKENDEITVT----VPEPEELDIRAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMYHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYQAIVHGVIPHDKGTIDAPIAR-DKKDRQSMAVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK---KTLNLNGQALHAGILGFNHPRTGEYLQFEAPAPAIFEE 295
>gi|82750802|ref|YP_416543.1| hypothetical protein SAB1061 [Staphylococcus aureus RF122] >gi|82656333|emb|CAI80750.1| conserved hypothetical protein [Staphylococcus aureus RF122] (305 aa)
Score = 371, Expect = 9.4e-34, Identities = 97/276 (35%), Positives = 160/276 (57%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           SR+  +  I+  LV  N K++ K N KV     I++ E+++VE    + P   +++I YED  + +V KP  ++VHP+    +NTL N + Y    K +      +R GIVHR+D  T GL++VAK+  +     +  +D+ +++KY+AL+H ++      +DAPI R   + R+ ++   D KEA T F  +  +K++TL E +L TGRTHQIRVH ++I   ++ DP YGPK   KT    GQ L A  + F HP T + +  + ++P++F++ +
  S:    30 SRNQIQDWIKAGLVVANDKVV-KSNYKVKLNDHIVVTEKEVVEAD--ILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMY--QIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRELVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGR-NKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPK---KTLDIGGQALHAGLIGFEHPVTGEYIERHAELPQDFEDLL 297
>gi|49478436|ref|YP_037954.1| ribosomal large subunit pseudouridine synthase D [Bacillus thuringiensis serovar konkukian str. 97-27] >gi|49329992|gb|AAT60638.1| ribosomal large subunit pseudouridine synthase D [Bacillus thuringiensis serovar konkukian str. 97-27] (302 aa)
Score = 371, Expect = 9.8e-34, Identities = 104/290 (35%), Positives = 163/290 (56%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +  +R+D  V+      SR+  +  I++++VTVNGK + K N KV E+ EI +   +   E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F++
  S:    13 QKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAV-KGNYKVREDDEITVTIPE--PEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIQFEAPIPEVFED 295
>gi|160902202|ref|YP_001567783.1| RluA family pseudouridine synthase [Petrotoga mobilis SJ95] >gi|160359846|gb|ABX31460.1| pseudouridine synthase, RluA family [Petrotoga mobilis SJ95] (319 aa)
Score = 371, Expect = 1.1e-33, Identities = 108/289 (37%), Positives = 172/289 (59%)
  Q:     5 QRLDILVSSKF--SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKV--LTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNF-TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +RLDI ++ K    +SR++ ++ I    +TVNG    KP+ KV +  EI +   ++VEETK   + P    + I+YED+ ++++NKP  +IVHPT    + TL N ++ ++ D  K     DP R+GIVHRLDK T G+++VAK+  S +  +K F ++K  K YLA++   L+ +  E++ P+ R     R + +   + KEA T +K + ++ +  TL  + L TGRTHQIRVH ++I N +I D +YG   I K  +     Q L A KL F HP T++ +     +P +FK  +
  S:    15 KRLDIYIAQKMPIEISRNLIQNAITKGQITVNGSQ-KKPHYKVKQGDEIQIDFHELVEETKEENILPENIPLNILYEDEELIVINKPAGLIVHPTPSIKTGTLVNALMHHVKDLDKTMQ--DPNRLGIVHRLDKETSGVLVVAKNAFSHHLLSKEFKERKTMKYYLAIVEGTLKEKEGEINLPLGR-HPILRHKRAVVYNGKEAITEYKTLKEFGDLATLVWIRLRTGRTHQIRVHFKYIGNPLIGDSLYGKNKIEKNLQIPVGRQMLHALKLGFYHPKTKEWMEFLAPLPDDFKNLL 308
>gi|163790406|ref|ZP_02184837.1| Pseudouridylate synthase, 23S rRNA-specific [Carnobacterium sp. AT7] >gi|159874310|gb|EDP68383.1| Pseudouridylate synthase, 23S rRNA-specific [Carnobacterium sp. AT7] (301 aa)
Score = 370, Expect = 1.2e-33, Identities = 109/294 (37%), Positives = 172/294 (58%)
  Q:     2 KNTQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + T RLD +++    S++RS  +  I+   VTVNG+ + K N KV    EI++ E ++V   +VL      IEIVY+D+ +++VNK   ++VHP++   + TL N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +         D+   ++Y+AL+H  +      +DAP+ R +   +++   D   +EA T F  + ++K+FTL  ++L TGRTHQIRVH ++I   +  DPIYGP+   KT +  GQ+L A  L F HP T + V     +P+ F++ + K
  S:    11 EETGRLDKVLTELLPSITRSHIQQWIKEGNVTVNGENL-KANYKVQPSDEIVIIEPELVS-LEVLAE-DIPIEIVYQDEDVVVVNKAQGMVVHPSAGHQTGTLVNALMYHIKDLSGI--NGT-IRPGIVHRIDKDTSGLLMVAKNDSAHEKLAAQLKDKTSLREYIALVHGVIPHEKGTIDAPLGRSKVDRKKQDIID-GGREAVTHFTVLERFKDFTLVSLKLETGRTHQIRVHMKYIGYPLAGDPIYGPR---KTLEGKGQFLHAQTLGFKHPTTGEFVTFEAPLPQLFEDTLTK 297
>gi|110004584|emb|CAK98921.1| probable pseudouridine synthase d protein [Spiroplasma citri] (306 aa)
Score = 370, Expect = 1.3e-33, Identities = 91/291 (31%), Positives = 173/291 (59%)
  Q:     1 MKNTQRLDILVSSKFS-----LSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYN--GDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           + ++ R+D +++  F       SR+  +  I+   V VNG+++ +   +++ +   I     K  E    LTP    + I+YED Y+++++KPN+++VHP     ++TL N +     ++ ++++      R GIVHR+D+ T G +I+AK+    +   +    ++++++YLAL+H  +     ++DAPI R   + ++ V    ++K+A T    I ++ ++T  E EL +GRTHQIR H ++I + ++ DP+YG    +K   +GQYL AY+L+FIHP T++ + I   +P+EF++
  S:     8 VSSSARIDKILTDYFKTNTTPFSRTKIQELIKQEKVQVNGQVVRANYVSQIGDHVIIEFPSAKASE----LTPLAIPLTILYEDSYLMVIDKPNNLVVHPAPGHQNDTLVNALL----ARGVQWSTASGEQRPGIVHRIDRQTTGTLIIAKNDVVHHQLQQQIQTKQLQRRYLALVHGQIIENRAKIDAPIGRDPNNRKKMVVTAKNSKKALTNIVVIERFNDYTYIECELESGRTHQIRAHLKYINHPIVGDPLYGTV-ADKKESFGQYLHAYQLRFIHPVTKESLTITAALPQEFEQ 297
>gi|65321221|ref|ZP_00394180.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus anthracis str. A2012] (302 aa)
Score = 369, Expect = 1.4e-33, Identities = 104/290 (35%), Positives = 162/290 (55%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +  +R+D  V+      SR+  +  I++++VTVNGK + K N KV E  EI +   +   E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F++
  S:    13 QKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAV-KGNYKVRENDEITVTIPE--PEELDIQPEDMNLEIYYEDADVLVVNKPRSMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIQFEAPIPEVFED 295
>gi|52141596|ref|YP_085233.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus E33L] >gi|51975065|gb|AAU16615.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus E33L] (302 aa)
Score = 369, Expect = 1.4e-33, Identities = 104/290 (35%), Positives = 162/290 (55%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +  +R+D  V+      SR+  +  I++++VTVNGK + K N KV E  EI +   +   E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F++
  S:    13 QKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAV-KGNYKVKENDEITVTIPE--PEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIQFEAPIPEVFED 295
>gi|50812225|ref|NP_389429.2| hypothetical protein BSU15460 [Bacillus subtilis subsp. subtilis str. 168] >gi|47606790|sp|Q45480|YLYB_BACSU Uncharacterized RNA pseudouridine synthase ylyB (RNA-uridine isomerase) (RNA pseudouridylate synthase) >gi|32468746|emb|CAB13420.2| ylyB [Bacillus subtilis subsp. subtilis str. 168] (303 aa)
Score = 369, Expect = 1.6e-33, Identities = 103/297 (34%), Positives = 167/297 (56%)
  Q:     2 KNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKK--DIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           + ++R+D  L S++   SR+  +  +++  V VNG  + K N K+    ++ +     V E + L    +  D++I YED+ +L+VNKP  ++VHP    L+ TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     +++ + +KY A++H  +      +DAPI R +   R+ ++   D K A T F  +  +++FTL E +L TGRTHQIRVH ++I   +  DP YGP+   KT  + GQ L A  L F HP T + V     +P++  E I+   K
  S:    12 QKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAV-KANYKIQPGDQVTVT----VPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLISHDDGTIDAPIGR-DKKDRQSMTVTRDGKNAVTHFHVLEGFQDFTLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPR---KTIDFNGQPLHAGVLGFDHPRTGEYVEFEAPLPEDMAELIENLRK 301
>gi|42782985|ref|NP_980232.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus ATCC 10987] >gi|49186742|ref|YP_029994.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne] >gi|118479113|ref|YP_896264.1| ribosomal large subunit pseudouridine synthase D [Bacillus thuringiensis str. Al Hakam] >gi|165872288|ref|ZP_02216925.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0488] >gi|166995451|ref|ZP_02261911.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus AH820] >gi|167636442|ref|ZP_02394741.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0442] >gi|167641146|ref|ZP_02399401.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0193] >gi|170688858|ref|ZP_02880061.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0465] >gi|170708814|ref|ZP_02899250.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0389] >gi|177654900|ref|ZP_02936617.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0174] >gi|190565878|ref|ZP_03018797.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis Tsiankovskii-I] >gi|196035788|ref|ZP_03103190.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus W] >gi|196045901|ref|ZP_03113130.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus 03BB108] >gi|42738912|gb|AAS42840.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Bacillus cereus ATCC 10987] >gi|49180669|gb|AAT56045.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne] >gi|118418338|gb|ABK86757.1| ribosomal large subunit pseudouridine synthase D [Bacillus thuringiensis str. Al Hakam] >gi|164711964|gb|EDR17504.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0488] >gi|167510926|gb|EDR86317.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0193] >gi|167528184|gb|EDR90971.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0442] >gi|170126299|gb|EDS95190.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0389] >gi|170667213|gb|EDT17973.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0465] >gi|172080411|gb|EDT65498.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0174] >gi|190562797|gb|EDV16763.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis Tsiankovskii-I] >gi|195991437|gb|EDX55403.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus W] >gi|196023341|gb|EDX62019.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus 03BB108] (302 aa)
Score = 369, Expect = 1.7e-33, Identities = 104/290 (35%), Positives = 162/290 (55%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +  +R+D  V+      SR+  +  I++++VTVNGK + K N KV E  EI +   +   E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F++
  S:    13 QKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAV-KGNYKVRENDEITVTIPE--PEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIQFEAPIPEVFED 295
>gi|116491102|ref|YP_810646.1| ribosomal large subunit pseudouridine synthase D [Oenococcus oeni PSU-1] >gi|116091827|gb|ABJ56981.1| ribosomal large subunit pseudouridine synthase D [Oenococcus oeni PSU-1] (304 aa)
Score = 369, Expect = 1.7e-33, Identities = 103/295 (34%), Positives = 170/295 (57%)
  Q:     1 MKNTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGK-IISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +  + RLD ++++ FS  SR+  K  I+ + V VNGK +++K    V +   +++K    V++T++L P K  ++IVYED  +++VNKP  ++VHP++    +TL N +  +  +     NG+  R GIVHR+DK T GL++VAK+  +    +      K  +KYLA++H +   +   + API R +   R++ +   + +EA T FK +  + N++L E  L TGRTHQIRVH  +I + V  DP+YGP+        GQYL A  L    P T KE++ +  +P  F++ + K
  S:    12 VNQSGRLDKILATDFSAFSRNQIKKLIDQDRVIVNGKPVLAK--YLVQDGDHVVIKVPP-VKKTELL-PEKIPLDIVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNAL--LSHAPLSTINGE-FRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFSEKRGTIKAPIDR-DPKNRQKQAVVANGREAITHFKVLESFSNYSLIEAVLETGRTHQIRVHMAYIGHPVAGDPLYGPR--KTLPGRGQYLFASSLSLTQPHTGKELSFSAPLPDYFQKMLLK 298
>gi|118586926|ref|ZP_01544359.1| pseudouridylate synthases, 23S RNA-specific [Oenococcus oeni ATCC BAA-1163] >gi|118432653|gb|EAV39386.1| pseudouridylate synthases, 23S RNA-specific [Oenococcus oeni ATCC BAA-1163] (308 aa)
Score = 369, Expect = 1.7e-33, Identities = 103/295 (34%), Positives = 170/295 (57%)
  Q:     1 MKNTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGK-IISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +  + RLD ++++ FS  SR+  K  I+ + V VNGK +++K    V +   +++K    V++T++L P K  ++IVYED  +++VNKP  ++VHP++    +TL N +  +  +     NG+  R GIVHR+DK T GL++VAK+  +    +      K  +KYLA++H +   +   + API R +   R++ +   + +EA T FK +  + N++L E  L TGRTHQIRVH  +I + V  DP+YGP+        GQYL A  L    P T KE++ +  +P  F++ + K
  S:    16 VNQSGRLDKILATDFSAFSRNQIKKLIDQDRVIVNGKPVLAK--YLVQDGDHVVIKVPP-VKKTELL-PEKIPLDIVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNAL--LSHAPLSTINGE-FRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFSEKRGTIKAPIDR-DPKNRQKQAVVANGREAITHFKVLESFSNYSLIEAVLETGRTHQIRVHMAYIGHPVAGDPLYGPR--KTLPGRGQYLFASSLSLTQPHTGKELSFSAPLPDYFQKMLLK 302
>gi|22537512|ref|NP_688363.1| ribosomal large subunit pseudouridine synthase D [Streptococcus agalactiae 2603V/R] >gi|76797703|ref|ZP_00779971.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae 18RS21] >gi|77414617|ref|ZP_00790757.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae 515] >gi|22534392|gb|AAN00236.1|AE014254_16 ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae 2603V/R] >gi|76586927|gb|EAO63417.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae 18RS21] >gi|77159330|gb|EAO70501.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae 515] (296 aa)
Score = 369, Expect = 1.8e-33, Identities = 102/293 (34%), Positives = 166/293 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII--LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  ++    LSRS A  +I+  +V VNG++  K    V E   I   + +E++++      P    ++I+Y+D  + +VNKP  ++VHP++   S TL N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +     +   D+K  +KYLA++H +L      ++API R +   R++ +     K A T F  + ++ ++TL E+ L TGRTHQIRVH  +I + +  DP+YGP+        GQ+L A  L F HP   + +  ++++P+ F+  ++K  K
  S:    11 RLDKALADNSELSRSQANEEIKKGIVLVNGQV-KKAKYTVQEGDRITFDIPKEEVLDYQAENIP----LDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIGRSDKD-RKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHPLAGDPVYGPR--KTLGGKGQFLHAQTLGFTHPSNGENLIFSVEVPEIFQTTLEKLRK 295
>gi|116514036|ref|YP_812942.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365] >gi|116093351|gb|ABJ58504.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365] (304 aa)
Score = 369, Expect = 1.8e-33, Identities = 98/289 (33%), Positives = 168/289 (58%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEE---SEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++ + + LSRS  K  ++   + VNGK  SK + KV ++     I+L  E +  E + +      ++IVYEDK +++VNKP  ++VHP +   S+TL N +  ++ ++ +  + +  R GIVHR+DK T GL++VAK+  +  +  K    +  +++YLA++H +       +DAPI R     R++++     K A T FK + +Y+ ++L E +L TGRTHQIRVH  +I + +  DP+YGP+       +GQ+L A  L F  P T + +  ++  P+ F++ +
  S:    14 QRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKK-SKVSYKVQKDDLIQVIVLPLEPLKLEAENIP-----LDIVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNAL--LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAEEEGTIDAPIGR-NPKDRKQMAVVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRVHMAYIGHPLAGDPLYGPR--KTLPGHGQFLHAKTLGFEQPSTGEWLEFSVQPPEIFQQTV 295
>gi|49483360|ref|YP_040584.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus MRSA252] >gi|49241489|emb|CAG40175.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus MRSA252] (305 aa)
Score = 368, Expect = 2.2e-33, Identities = 100/276 (36%), Positives = 163/276 (59%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           SR+  +  I+  LV  N K++ K N KV     I++ E+++VE    + P   +++I YED  + +V KP  ++VHP+    +NTL N + Y I D   I  NG+ +R GIVHR+D  T GL++VAK+  +     +  +D+ +++KY+AL+H ++      +DAPI R   + R+ ++   D KEA T F  +  +K++TL E +L TGRTHQIRVH ++I   ++ DP YGPK   KT    GQ L A  + F HP T + +  + ++ ++F++ +
  S:    30 SRNQIQDWIKAGLVVANDKVV-KSNYKVKLNDHIVVTEKEVVEAD--ILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKDLSGI--NGE-IRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGR-NKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPK---KTLDIGGQALHAGLIGFEHPVTGEYIERHAELAQDFEDLL 297
>gi|76787790|ref|YP_330006.1| ribosomal large subunit pseudouridine synthase A [Streptococcus agalactiae A909] >gi|77408235|ref|ZP_00784979.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae COH1] >gi|77412105|ref|ZP_00788430.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae CJB111] >gi|76562847|gb|ABA45431.1| ribosomal large subunit pseudouridine synthase, RluA family [Streptococcus agalactiae A909] >gi|77161861|gb|EAO72847.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae CJB111] >gi|77173176|gb|EAO76301.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae COH1] (296 aa)
Score = 368, Expect = 2.4e-33, Identities = 102/293 (34%), Positives = 165/293 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEII--LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  ++    LSRS A  +I+  +V VNG++  K    V E   I   + +E++++      P    ++I+Y+D  + +VNKP  ++VHP++   S TL N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +     +   D+K  +KYLA++H +L      ++API R +   R++ +     K A T F  + ++ ++TL E+ L TGRTHQIRVH  +I + +  DP+YGP+        GQ+L A  L F HP   + +  ++++P+ F+  + K  K
  S:    11 RLDKALADNSELSRSQANEEIKKGIVLVNGQV-KKAKYTVQEGDRITFDIPKEEVLDYQAENIP----LDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIGRSDKD-RKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHPLAGDPVYGPR--KTLGGKGQFLHAQTLGFTHPSNGENLIFSVEVPEIFQTTLDKLRK 295
>gi|192812126|ref|ZP_03040795.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC10] >gi|192799273|gb|EDV75784.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC10] (324 aa)
Score = 368, Expect = 2.4e-33, Identities = 96/277 (34%), Positives = 149/277 (53%)
  Q:    17 LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILK--EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +SRS  +  I +  V+VN   I K N KV +   I+LK  E   VE    + P    +EI +ED  +++VNKP  ++VHP     S TL N +  +F  K +      LR GIVHR+DK T GL++ AK+  +  +      +  + ++YLAL+H ++      +DAPI R     +     D ++K A T F  + ++ +++L E++L TGRTHQIRVH ++I + ++ DP+YG     K    GQ L A  L F+HP T +    +  MP +  E +
  S:    49 VSRSQVQLWIADGHVSVNDGPI-KSNYKVSQGDRIVLKVPEPSAVE----IIPEDIPLEIAFEDGDVIVVNKPRGMVVHPAPGHSSGTLVNAL--MFHCKDLSGINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEHSVNRRYLALVHGNISHDQGTIDAPIGRDAQDRKLYTVTDRNSKHAVTHFTVVERFGDYSLLELKLETGRTHQIRVHMKYIGHPLVGDPVYGKSKGIKLN--GQALHAAVLGFVHPSTGEYKEFSAPMPSDMNELL 318
>gi|56419681|ref|YP_146999.1| hypothetical protein GK1146 [Geobacillus kaustophilus HTA426] >gi|56379523|dbj|BAD75431.1| hypothetical conserved protein [Geobacillus kaustophilus HTA426] (304 aa)
Score = 367, Expect = 2.6e-33, Identities = 99/289 (34%), Positives = 163/289 (56%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +R+D ++++     SRS  +  I+N LVTVNG+ + K N K +    + +   +   E   + P    ++I YED+ +L+VNKP  ++VHP    +  TL N ++ +  D   I  NG  LR GIVHR+DK T GL++VAK+  +  +  +  +++ + ++Y A++H  +      +DAPI R +   ++    + + KEA T F+ + +++++T  E +L TGRTHQIRVH ++I   +  DP YGPK   KT    GQ L A  L F HP + + +     +P EF E +
  S:    15 ERIDKVIAALNEEWSRSQVQQWIKNGLVTVNGQTV-KANYKCEAGDSVAVSPPE--PEPLHVEPEPIPLDIYYEDEDVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCRDLSGI--NG-VLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKAIVHGVIPHDYGTIDAPIGRDKRDRKKMAVTEENGKEAVTHFRVLERFRHYTYVECQLETGRTHQIRVHMKYIGYPLAGDPQYGPK---KTLAIDGQALHAGVLGFRHPRSGEYLEFEAPLPPEFAELL 297
>gi|77406381|ref|ZP_00783442.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae H36B] >gi|77175005|gb|EAO77813.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Streptococcus agalactiae H36B] (296 aa)
Score = 367, Expect = 2.8e-33, Identities = 103/293 (35%), Positives = 164/293 (55%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  ++    LSRS A  +I+  +V VNG++  K    V E   I       + + +VL    ++I  +I+Y+D  + +VNKP  ++VHP++   S TL N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +     +   D+K  +KYLA++H +L      ++API R +   R++ +     K A T F  + ++ ++TL E+ L TGRTHQIRVH  +I + +  DP+YGP+        GQ+L A  L F HP   + +  ++++P+ F+  + K  K
  S:    11 RLDKALADNSELSRSQANEEIKKGIVLVNGQV-KKAKYTVQEGDRITFD----IPKKEVLDYQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDQGVIEAPIGRSDKD-RKKQAVTAKGKPAVTRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHPLAGDPVYGPR--KTLGGKGQFLHAQTLGFTHPSNGENLIFSVEVPEIFQTTLDKLRK 295
>gi|147678153|ref|YP_001212368.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI] >gi|146274250|dbj|BAF59999.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI] (312 aa)
Score = 367, Expect = 3.0e-33, Identities = 97/291 (33%), Positives = 164/291 (56%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILK--EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +RLD+ ++ +   L+R+  +  I   + +VNG+   + + +V     ++L+  E + +E  K   P    +E+ YED  ++++NKP  ++VHP   + S TL N + Y   S     NG  +R GIVHRLDK T GL++VAK+  +  +  +   +++I ++YLAL+H  L+ ++  VDAPI R     ++      +AK+A T ++ + ++K +T  E+ L TGRTHQIRVH  +I + V+ D  YGP   +   + GQ+L A  L F HP T + +     +P   K  ++K
  S:    16 KRLDLFLAGEMEGLTRTYVQKLIAEGMASVNGQR-GRASYRVKPGDVVVLQVPEPEGLEIKKEPIP----LEVYYEDADVIVINKPRGMVVHPADGNYSGTLVNALLY-HCSDLSGING-VMRPGIVHRLDKDTSGLIMVAKNDTAHLSLARQLKERQITRRYLALVHGLLKEQSGMVDAPIGRDPRDRKKMAVLQKNAKQAVTRYRVLERFKGYTYIELMLETGRTHQIRVHMSYIGHPVVGDLKYGPSRPHFGLE-GQFLHAAVLGFHHPRTGEYLQFEAPLPDVLKAVLEK 301
>gi|124520889|ref|ZP_01695961.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1] >gi|124497258|gb|EAY44823.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1] (303 aa)
Score = 367, Expect = 3.1e-33, Identities = 101/285 (35%), Positives = 156/285 (54%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           +RLD +VSS +   SRS  +  I++  +TVNGK   K N ++  ++  +++ E    E   + P    ++I YED  +L+VNKP  ++VHP++   + TL N + Y    K +      LR GIVHR+DK T GL++VAK+  +         ++ + +KY AL+H ++      +DAPI R     +R    D + K+A T F  + ++  +T  E  L TGRTHQIRVH ++I + +  DP YGPK   KT  + GQ L A  L F HP T + +     +P +F
  S:    15 ERLDKMVSSIREEWSRSQVQQWIKDGDITVNGKK-EKANYRL--QTGDLVEIEVPEPELPDIEPEDLHLDIYYEDADVLVVNKPKGMVVHPSNGHFTGTLVNGLMY--HCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDYAHEKLAAQLSEKTVTRKYFALVHGNIPHEAGTIDAPIGRDPADRQRMAVVD-NGKDAVTHFHVLERFDRYTFIECRLETGRTHQIRVHMKYIGHPLAGDPKYGPK---KTIDFGGQALHAGVLGFCHPRTGETLTFEAPLPDDF 292
>gi|196038675|ref|ZP_03105983.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus NVH0597-99] >gi|196030398|gb|EDX68997.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus NVH0597-99] (302 aa)
Score = 367, Expect = 3.2e-33, Identities = 104/290 (35%), Positives = 162/290 (55%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           +  +R+D  V+      SR+  +  I++++VTVNGK + K N KV E  EI +   +   E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F++
  S:    13 QKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAV-KGNYKVRENDEITVTIPE--PEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVIRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIQFEAPIPEVFED 295
>gi|167765516|ref|ZP_02437580.1| hypothetical protein CLOSS21_00010 [Clostridium sp. SS2/1] >gi|167712701|gb|EDS23280.1| hypothetical protein CLOSS21_00010 [Clostridium sp. SS2/1] (305 aa)
Score = 366, Expect = 3.3e-33, Identities = 105/291 (36%), Positives = 167/291 (57%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKV-LTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN-FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +RLD+++S + S L+RS      +     +NGK  SK N K  E   I L+   + E T++ + P + +++IVYED+ ++++NKP  ++VHP +   S TL N +           NG  LR GIVHR+DK T G++IV K+  +  +  K   D  I +KY A+++ +++     V+API R     R+++   +D K A T +K + + K  FT  E +L TGRTHQIRVH   IK+ ++ D +YGPK  +K T  GQ L A  L F+HP T + +   + +P+ F++ + K
  S:    16 KRLDVVLSEQCSDLTRSYINKLCKEERAALNGKT-SKGNKKCKEGDVITLQ---VPEPTELEILPEEMNLDIVYEDQDVILINKPKGMVVHPAAGHYSGTLVNGLMAHCKDDLSGING-VLRPGIVHRIDKDTTGILIVCKNDMAHQSIAKQLYDHSITRKYHAIVYGNIKEEEGTVNAPIGR-SLKDRKKMGIVMDGKHAVTHYKVLKRLKKGFTYIECQLETGRTHQIRVHMASIKHPLLGDDVYGPKK-SKYTLEGQCLHAKVLGFVHPRTGEYMEFEVPLPEYFEKLLNK 302
>gi|138894673|ref|YP_001125126.1| ribosomal large subunit pseudouridine synthase D-like protein [Geobacillus thermodenitrificans NG80-2] >gi|196247711|ref|ZP_03146413.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16] >gi|134266186|gb|ABO66381.1| ribosomal large subunit pseudouridine synthase D-like protein [Geobacillus thermodenitrificans NG80-2] >gi|196212495|gb|EDY07252.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16] (304 aa)
Score = 366, Expect = 3.5e-33, Identities = 98/290 (33%), Positives = 161/290 (55%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D ++++     SRS  +  I+N LVTVNG+ + K N K +    + +   +   E   + P    ++I YED+ +L+VNKP  ++VHP    +  TL N ++ +  D   I  NG  LR GIVHR+DK T GL++VAK+  +  +  +  +++ + ++Y A++H  +      +DAPI R +   ++    D + KEA T F+ + +++ +T  E +L TGRTHQIRVH ++I   +  DP YGPK     +  GQ L A  L F HP +   +     +P EF E ++
  S:    15 ERIDKVIAALNDEWSRSQVQQWIKNGLVTVNGRTV-KANYKSELGDTVAISPPE--PEPLHVEPEPIPLDIYYEDEDVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCRDLSGI--NG-VLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKAIVHGVIPHDYGTIDAPIGRDKRDRKKMAVTDENGKEAVTHFRVLERFRQYTYVECQLETGRTHQIRVHMKYIGYPLAGDPQYGPK--KTLSIEGQALHAGVLGFRHPRSGDYLEFEAPLPPEFAELLE 298
>gi|163814069|ref|ZP_02205461.1| hypothetical protein COPEUT_00222 [Coprococcus eutactus ATCC 27759] >gi|158450518|gb|EDP27513.1| hypothetical protein COPEUT_00222 [Coprococcus eutactus ATCC 27759] (304 aa)
Score = 366, Expect = 3.6e-33, Identities = 98/291 (33%), Positives = 158/291 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN-FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +RLD ++S  F   SRS  K   ++ L+ VN K + KP+ KV     I +     V     + P    ++I+YED  +++VNKP  ++VHP     S TL N + Y F S     NG+  R GIVHR+D  T G+++V K+ ++  A ++   +  I +KY A+++ ++ +    VDAPI R     ++    + + + A T ++ + ++   +T  E +L TGRTHQIRVH   I + ++ D +YGPK      + GQ L A  L FIHP T + V    ++P+ FK  ++K
  S:    15 RRLDKVLSEYFDGYSRSFIKKLFDDGLILVNSKAV-KPSYKVRAGDMIDISVPDPVSID--IVPEDIPLDIIYEDDDVILVNKPKGMVVHPAPGHYSGTLVNGLMYHFGSSLSGINGE-FRPGIVHRIDMDTTGVLVVCKNDNAHRALSEQLHEHSITRKYYAIVYGNISSDEGTVDAPIGRSPKDRKKMAINNRNGRRAVTHYRVLERFGGRYTYIECQLETGRTHQIRVHMASIGHPILGDEVYGPKKCPFKLQ-GQTLHAGVLGFIHPSTGEYVEFKAELPEYFKAVLEK 302
>gi|169350183|ref|ZP_02867121.1| hypothetical protein CLOSPI_00927 [Clostridium spiroforme DSM 1552] >gi|169292966|gb|EDS75099.1| hypothetical protein CLOSPI_00927 [Clostridium spiroforme DSM 1552] (306 aa)
Score = 366, Expect = 3.6e-33, Identities = 101/288 (35%), Positives = 158/288 (54%)
  Q:     3 NTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKI-ISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           N  RLD +++     LSR+  +  I   LV VNGK+  +   TK++++ EI +++   +E      P    + +VYEDK +++++KP  +IVHP+    S TL N +  +F  K +       R GIVHR+DK T GL++VAK+  +    ++   D  + ++Y+AL+H  +     ++DAPI R     +       ++K A T F  + +YKN +L E  L TGRTHQIRVH  +I   V  DP YG +       +GQ+L A KL FIHP T++ +    ++P  FK
  S:    12 NNYRLDKIIALNMEELSRTQIQEMIGRGLVLVNGKVEKASYKTKLNDQIEITIEDNSDLEIEAEDIP----LNVVYEDKDVIVIDKPTGMIVHPSPGITSGTLVNAL--LFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDIAHRFLSEQLKDHSVTRRYVALVHGLIPHVQGKIDAPIGRNPNDRQSMCVTKNNSKNAITNFTVLKRYKNMSLIECRLETGRTHQIRVHMSYIGYPVYGDPKYGYR--KDDCSHGQFLHAKKLGFIHPTTKEYMEFESELPDYFK 293
>gi|126647249|ref|ZP_01719759.1| ribosomal large subunit pseudouridine synthase D [Algoriphagus sp. PR1] >gi|126577297|gb|EAZ81545.1| ribosomal large subunit pseudouridine synthase D [Algoriphagus sp. PR1] (344 aa)
Score = 365, Expect = 4.8e-33, Identities = 102/291 (35%), Positives = 169/291 (58%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDI-----DAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           R+D  +S K +  +R+  +  I+   V VNGK  +K N K+    +I +  EK   +T+V  P K +++I+YEDKY+LIVNKP  ++VHP   + S TLAN + Y F D  ++K  G+  R G+VHR+DK T GL+++AK  ++       F    I++ Y+AL+    +     ++  + R   S +     D+       K A T +K + + +  +L +  L TGRTHQIR H ++I + + ND +YG   I K T++ +Y               L A  L FIHP ++++V   + +PK+F + ++K+
  S:    32 RIDKFLSEKLANATRNKVQQAIDAGSVLVNGKP-TKANYKIKPMDDIKVMMEKPPRDTEVY-PEKIELDIIYEDKYLLIVNKPAGMVVHPAHGNWSGTLANALVYHFQDLPEMK--GNEGRPGLVHRIDKDTSGLLVIAKQEEAMTHLASQFFHHTIDRTYIALVWGEPKEDEGTIEGNVGR---SAKNRKVMDVFPDGEQGKHAITHWKVLKRLRYVSLIQCNLETGRTHQIRAHMKYIGHPLFNDAMYGGDKIRKGTQFSKYKTFVQNCFDLIPRQALHAMSLGFIHPVSKEKVYYEVGLPKDFADVLEKW 337
>gi|160892655|ref|ZP_02073445.1| hypothetical protein CLOL250_00185 [Clostridium sp. L2-50] >gi|156865696|gb|EDO59127.1| hypothetical protein CLOL250_00185 [Clostridium sp. L2-50] (305 aa)
Score = 365, Expect = 5.3e-33, Identities = 105/291 (36%), Positives = 160/291 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN-FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  ++  F + SRS  K  +++  + VN K  +KP+ K+     I +    I   +  + P    ++IVYED+ I+IVNKP  ++VHP     S TL N + Y F       NG+ LR GIVHR+D  T GL++V K+  + N  ++      I +KY A+  N+       VD PI R  T  ++      + + A T +K + K KN F L E +L TGRTHQIRVH  +IK+ ++ D IYGPK+       GQ L A  L FIHP T++ V  + ++P+ F++ +K+
  S:    15 KRVDKGLADYFDNYSRSFLKKLLDDGNILVNDKK-AKPSLKIASGDRIDITIPSIA--SVEIEPENIPLDIVYEDEDIIIVNKPKGMVVHPAPGHYSGTLVNGLMYHFKDSLSGINGE-LRPGIVHRIDMDTTGLLVVCKNDAAHNFLSEQLAVHSITRKYYAICFNYFTEDEGIVDLPIGRHPTDRKKMAVNYKNGRNAVTHYKVLKKLKNNFCLIECQLETGRTHQIRVHMSYIKHPLLGDAIYGPKN-QPYHLQGQTLHAGVLGFIHPSTKEYVEFSSELPEYFQKLLKQ 302
>gi|21282809|ref|NP_645897.1| hypothetical protein MW1080 [Staphylococcus aureus subsp. aureus MW2] >gi|49486036|ref|YP_043257.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus MSSA476] >gi|21204247|dbj|BAB94945.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus MW2] >gi|49244479|emb|CAG42908.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus MSSA476] (305 aa)
Score = 365, Expect = 5.3e-33, Identities = 96/276 (34%), Positives = 159/276 (57%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           SR+  +  I+  LV  N K++ K N KV     I++ E+++VE    + P   +++I YED  + +V K   ++VHP+    +NTL N + Y    K +      +R GIVHR+D  T GL++VAK+  +     +  +D+ +++KY+AL+H ++      +DAPI R   + R+ ++   D KEA T F  +  +K++TL E +L TGRTHQIRVH ++I   ++ DP YGPK   KT    GQ L A  + F HP T + +  + ++P++F++ +
  S:    30 SRNQIQDWIKAGLVVANDKVV-KSNYKVKLNDHIVVTEKEVVEAD--ILPENLNLDIYYEDDDVAVVYKTKGMVVHPSPGHYTNTLVNGLMY--QIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGR-NKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPK---KTLDIGGQALHAGLIGFEHPVTGEYIERHAELPQDFEDLL 297
>gi|109645926|ref|ZP_01369846.1| pseudouridine synthase, RluA family [Desulfitobacterium hafniense DCB-2] >gi|109643875|gb|EAT53428.1| pseudouridine synthase, RluA family [Desulfitobacterium hafniense DCB-2] (334 aa)
Score = 364, Expect = 6.1e-33, Identities = 97/268 (36%), Positives = 147/268 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIIL-----KEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHP 273
           RLD+ V+ +   SRS  +  IE   V VNG    K N KV    +I +     +E K+  E   L       EI+YED+ +L+VNK   ++VHP     + TL N +  ++  + +      LR GIVHR+DK T GL++VAK+  +     +      + ++YLA++H  +   +  V+API R     ++      +AKEA T ++ + ++++FTL E  L TGRTHQIRVH  ++K+ V+ DP+YGP+  N     GQ L A  L F HP
  S:    44 RLDVGVTERVGKSRSFIQGLIEEGHVLVNGAA-RKANYKVRAMDQIAVVIPPPRELKVEAENIPL-------EILYEDEDVLVVNKSQGMVVHPAPGAWTKTLVNAL--LYHCRNLSGINGVLRPGIVHRIDKDTSGLLVVAKNDLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTVEAPIGRDPADRKKMAVVFQNAKEAVTHYEVLERFRDFTLLEARLETGRTHQIRVHMAYLKHPVLGDPLYGPRK-NPFGLQGQMLHAQLLGFQHP 305
>gi|94992202|ref|YP_600301.1| ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS2096] >gi|94545710|gb|ABF35757.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus pyogenes MGAS2096] (223 aa)
Score = 364, Expect = 7.0e-33, Identities = 86/223 (38%), Positives = 136/223 (60%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           ++I+YED  + I+NKP  ++VHP++   S T+ N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +  A  +    +K  +KYLA++H +L      ++API R E   R++ +     KEA T F  + ++ +++L E++L TGRTHQIRVH  +I + V  DP+YGP+     + +GQ+L A  L   HP T KE+   ++ P+ F++ +K
  S:     1 MDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKD-RKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR--KTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLK 218
>gi|159029548|emb|CAO87700.1| rluD [Microcystis aeruginosa PCC 7806] (308 aa)
Score = 363, Expect = 7.3e-33, Identities = 93/289 (32%), Positives = 156/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEES--EIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRRE--VSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +RLD  + S+   LSRS  +  IE   + +NG+I +  NTKV +    +I + + + ++    L+    D++I+YED+Y++I+NKP D++VHP     S TL N +  +     +   G   R GIVHRLDK T G +++AK+  +          +   ++Y+AL+H   ++ T  +D PI R  +  ++   ++ +   + A T ++   +  N+TL E  L TGRTHQIRVH+  I + ++ DP+Y           GQ L AY+L  IHP T + +     +P  F + +
  S:    13 ERLDAWMGSQLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQGDRLKITIPDSQPLQ----LSAEAIDLDILYEDEYLIIINKPADLVVHPAPGHESGTLVNAL--LHHCPNLAGIGGIQRPGIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYMALVHGVPKSETGTIDLPISRHRSDRQKMAIIAVEKGGRNAVTHWQVKERLGNYTLMEFRLETGRTHQIRVHSSHIGHPILGDPLYSSGRSIGINLPGQLLHAYRLILIHPVTGESLEAIAPLPAIFPKVL 300
>gi|15615105|ref|NP_243408.1| hypothetical protein BH2542 [Bacillus halodurans C-125] >gi|10175162|dbj|BAB06261.1| BH2542 [Bacillus halodurans C-125] (305 aa)
Score = 363, Expect = 8.3e-33, Identities = 98/291 (33%), Positives = 162/291 (55%)
  Q:     5 QRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  L +     SR+  +  I++  V +NG+ I K N KV+  +  E+ + E +++E    + P    IEI+YED+ + +VNKP  ++VHP     + TL N + Y      +      +R GIVHR+DK T GL+++AK+  +  +       +  E+ Y A++H ++      +DAPI R +   +     + ++++A T F  + ++ +FT  E +L TGRTHQIRVH ++I   +  DP YGPK   KT    GQ L A KL F HP T + +   ++MP+E K+ I++
  S:    16 ERIDKFLTAQGEEWSRTQVQQWIKDGHVLINGRTI-KSNYKVETGDTLELFVPEPEVLE----VVPENIPIEIIYEDEDVAVVNKPRGMVVHPAPGHTTGTLVNALMY--HCNDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDRAHESLVNQLKAKTTERVYQAIVHGNIPHDHGTIDAPIGRDKVDRQSMTVTEENSRDAVTHFTVLERFGDFTFVECQLETGRTHQIRVHFKYIGFPLAGDPKYGPK---KTLSIDGQALHAQKLGFEHPRTGEFMRFKVEMPEEMKKLIRQ 300
>gi|47570307|ref|ZP_00240954.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus G9241] >gi|47553016|gb|EAL11420.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus G9241] (302 aa)
Score = 363, Expect = 8.7e-33, Identities = 105/290 (36%), Positives = 164/290 (56%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           + ++R+D  V+      SRS  +  I++++VTVNGK + K N KV E  EI +     EE  ++   +      ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F++
  S:    13 QKSERIDKFVAEINGEWSRSQVQQWIKDDVVTVNGKSV-KVNYKVKENDEITVTIPDPEELDIQAEDM------NLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIQFEAPIPEVFED 295
>gi|167745608|ref|ZP_02417735.1| hypothetical protein ANACAC_00300 [Anaerostipes caccae DSM 14662] >gi|167654920|gb|EDR99049.1| hypothetical protein ANACAC_00300 [Anaerostipes caccae DSM 14662] (305 aa)
Score = 362, Expect = 9.4e-33, Identities = 103/292 (35%), Positives = 166/292 (56%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDA-KEARTIFKEINKYKN-FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           RLD+ ++ +F   +RS  +   +++ V V+     K N KV E   +ILK  K  E +  + P K D++IVYED+ I+++NKP +++VHP       TL N +      +    NG  LR GIVHR+DK T G++IV K+  +     +   D  I ++Y A++ ++++  +  VDAPI R     R++++ D +A + A T ++ + + K  FT  E  L TGRTHQIRVH   I + ++ D +YGPK  +K +  GQ L A  L F HP T++ +   + +P  F+E +K+ G
  S:    17 RLDVCLAGRFPEFTRSYLQKLCKDSAVLVDDAE-KKSNYKVREGERVILKVPKPTELS--IKPEKMDLDIVYEDRDIILINKPKNMVVHPAPGHYEGTLVNGLMEHCRDELSGING-VLRPGIVHRIDKDTTGILIVCKNDMAHQCLAEQLKDHTITRRYHAIVCHNIKEESGTVDAPIAR-SRKDRKKMAIDREAGRRAVTHYRVLERLKEGFTYIECRLETGRTHQIRVHMASIGHPLLGDTVYGPKK-SKYSLEGQCLHAKVLGFTHPRTKEYMEFEVGLPAYFEELLKRLG 305
>gi|121533717|ref|ZP_01665544.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans Nor1] >gi|121307708|gb|EAX48623.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans Nor1] (309 aa)
Score = 362, Expect = 9.4e-33, Identities = 96/291 (32%), Positives = 162/291 (55%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILK--EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +RLD+ +  +   LSR+  +  I    VTVNGK   K N K+     + ++  E K  E    +      ++I+YED+ I+++NKP  ++VHP + +   TL N +    D +    NG   R GIVHRLDK T G+++VAK+  +     +   ++   +KY+A++H +++     ++API R  T  ++      ++KEA T F+ + ++ ++TL E  LFTGRTHQIRVH  +I + V+ DP YGP    +    GQ L A +L F HP T + ++  + +P + +  +++
  S:    20 KRLDLFLVERLPELSRTHIQRIIAAGEVTVNGKA-GKANYKLAPADYVTIRLPEPKPAE----IKAEAISLDILYEDEDIIVINKPRGMVVHPAAGNYEGTLVNALLRHCD-RLSGINGVS-RPGIVHRLDKDTSGVMMVAKTDRAHLDLARQIKERTAGRKYVAIVHGNIKENQGIINAPIGRHPTDRKKMAVVFTNSKEAITTFQVLERFGDYTLVECRLFTGRTHQIRVHMAYIGHPVVGDPKYGPGR-QRFAIMGQALHAAELTFQHPVTGERMSFTVPLPDDMRAILEE 305
>gi|126649705|ref|ZP_01721941.1| YlyB [Bacillus sp. B14905] >gi|126593424|gb|EAZ87369.1| YlyB [Bacillus sp. B14905] (303 aa)
Score = 362, Expect = 1.0e-32, Identities = 97/291 (33%), Positives = 161/291 (55%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  +SS +   SR+   + + +  + VNG  + KP  KV +  ++I  +    E   V+      ++IVYED  +L+VNKP  ++VHP    L+ TL N + Y    K +      +R GIVHR+DK T GL++VAK+  +  +     +++ + +KY+AL+H H+      +DAPI R +   +++   D + K A T F  + ++ ++TL E  L TGRTHQIRVH  +I   ++ DP YGPK   KT  + GQ L A  L F HP + + +     +P ++++ + +
  S:    15 ERIDKALSSLQSEWSRTQIGNWVSDGNIKVNGDAV-KPKYKV-KAGDVIAIDVPEAEPLDVIAE-NLALDIVYEDADVLVVNKPKGMVVHPAPGHLTGTLVNGLMY--QCKDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNKTVTRKYIALVHGHIAHDKGTIDAPIGRDQKDRQKQAIVD-NGKHAVTHFHVVERFGDYTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPK---KTIDFGGQVLHAATLGFNHPSSGEYLEFETPLPADYEQLLNE 298
>gi|167630173|ref|YP_001680672.1| RluA family pseudouridine synthase [Heliobacterium modesticaldum Ice1] >gi|167592913|gb|ABZ84661.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum Ice1] (369 aa)
Score = 361, Expect = 1.5e-32, Identities = 103/289 (35%), Positives = 162/289 (56%)
  Q:     6 RLDI-LVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY--KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           R+D+ LV      SRS  ++ I+  LVT++G  + K N ++    ++I       E  ++L P    +EI+++D  I ++NKP  ++VHP     S TL N + Y I D   I  NG+ LR GIVHR+DK T GL++VAK+  +    T+   D ++ ++YLA++H  +   T  V+API R +   R+ ++     K A T F+ + +Y  + F+L    L TGRTHQIRVH   I + V  DP YGP+        GQ L A+KL+F+HP + + +    D P+ F + ++
  S:    48 RVDVWLVQKGLVPSRSHGQNWIKEGLVTLDGGPL-KANYRL-RPGDVIEVAPPAPEAVEIL-PEDIPLEIIFQDADIAVINKPAGLVVHPAEGHWSGTLVNALLYHIKDLSGI--NGE-LRPGIVHRIDKDTSGLLVVAKNDRAHIHLTEQVKDHRVRREYLAVVHGVIGAETGRVEAPIGR-DPKDRQRMAVIAGGKSAITHFRVLARYPEQGFSLLHCRLETGRTHQIRVHLAHIGHPVAGDPKYGPRKAAFGLT-GQALHAWKLEFVHPRSGEPMRFQADPPEPFVQVLQ 332
>gi|104774018|ref|YP_618998.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842] >gi|103423099|emb|CAI97824.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842] (303 aa)
Score = 360, Expect = 1.7e-32, Identities = 98/289 (33%), Positives = 168/289 (58%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEE---SEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++ + + LSRS  K  ++   + VNGK  SK + KV ++     I+L  E +  E + +      ++IVYEDK +++VNKP  ++VHP +   S+TL N +  ++ ++ +  + +  R GIVHR+DK T GL++VAK+  +  +  K    +  +++YLA++H +       +DAPI R     R++++     K A T FK + +Y+ ++L E +L TGRTHQIRVH  +I + +  DP+YGP+       +GQ+L A  L F  P T + +  ++  P+ F++ +
  S:    14 QRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKK-SKVSYKVQKDDLIQVIVLPLEPLKLEAENIP-----LDIVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNAL--LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAEEGT-IDAPIGR-NPKDRKQMAVVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRVHMAYIGHPLAGDPLYGPR--KTLPGHGQFLHAKTLGFEQPSTGEWLEFSVQPPEIFQQTV 294
>gi|25011477|ref|NP_735872.1| hypothetical protein gbs1435 [Streptococcus agalactiae NEM316] >gi|24413015|emb|CAD47094.1| unknown [Streptococcus agalactiae NEM316] (296 aa)
Score = 360, Expect = 1.8e-32, Identities = 105/293 (35%), Positives = 168/293 (57%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEI---ILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  ++    LSRS A  +I+  +V VNG++  K    V E   I   I KEE +  + + ++     ++I+Y+D  + +VNKP  ++VHP++   S TL N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +     +   D+K  +KYLA++H +L      ++API R +   R++ +     K A T F  + ++ ++TL E+ L TGRTHQIRVH  +I + +  D +YGP+   KT +  GQ+L A  L F HP   + +  ++++P+ F+  + K  K
  S:    11 RLDKALADNSELSRSQANEEIKKGIVLVNGQV-KKAKYTVQEGDRITFDIPKEEVLDYQAENIS-----LDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIGRSDKD-RKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHPLAGDSVYGPR---KTLEGKGQFLHAQTLGFTHPSNGENLIFSVEVPEIFQTTLDKLRK 295
>gi|85057870|ref|YP_456786.1| ribosomal large subunit pseudouridine synthase D [Aster yellows witches'-broom phytoplasma AYWB] >gi|84789975|gb|ABC65707.1| ribosomal large subunit pseudouridine synthase D [Aster yellows witches'-broom phytoplasma AYWB] (306 aa)
Score = 360, Expect = 1.9e-32, Identities = 99/292 (33%), Positives = 159/292 (54%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           QRLD  +S+  +L++S  +  I    V VN K  SK +  +  +  I +   +  E   + TP   +++I+YED Y+ ++NKP +++VHP+      TL N + + F++     + D  R GIVHRLDK T GL+IVAK+ D  +     F  +KI K Y AL+   L+ + + +  PI R     R ++    D K A T FK + ++ +F+L E  L TGRTHQ+R H  F+K+ ++ D +Y   H    T  GQ+L +  LKF HP T + + +   +P  F++ +K +
  S:    16 QRLDHFLSAHINLNKSQCQKLILAQQVLVNTKS-SKKSYLLKPQDLITVIIPQTHESINLQTPQNLNLDIIYEDPYLAVINKPANLVVHPSLSFQKTTLVNGLLHQFNTLS---HIDTQRPGIVHRLDKNTTGLLIVAKTNDVSDKLQIAFQQRKITKIYWALIEGFLEDKGI-IKLPIGR-NNHNRLKMQVMPDGKTAVTHFKTLQRFSHFSLMECNLETGRTHQLRAHFSFLKHPIVGDLLYDSSH--HITPLGQFLHSKILKFNHPITNQNLILEAPLPTNFEKLLKTF 299
>gi|167755826|ref|ZP_02427953.1| hypothetical protein CLORAM_01342 [Clostridium ramosum DSM 1402] >gi|167704765|gb|EDS19344.1| hypothetical protein CLORAM_01342 [Clostridium ramosum DSM 1402] (306 aa)
Score = 360, Expect = 1.9e-32, Identities = 102/288 (35%), Positives = 158/288 (54%)
  Q:     3 NTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKI-ISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           N  RLD +++ +   LSR+  +  I   LV VN K   +   TK+++E EI + +   ++    + P    ++IVYED+ +++V+KP  +IVHP++  +  TL N +  +F  K +       R GIVHR+DK T GL++VAK+ ++    +K   D  + ++Y+AL+H  +     +VDAPI R     +       ++KEA T F  + +Y   +L E  L TGRTHQIRVH  +I   V  DP YG +       +GQ+L A KL FIHP TQK +     +P  F+
  S:    12 NNLRLDKVIAMQLQELSRTQIQDMINQGLVLVNQKKEKASYKTKLNDEIEITILDNVDLD----IEPEDISLKIVYEDEDVIVVDKPTGMIVHPSAGIMHGTLVNAL--LFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDNAHRLLSKQLKDHTVVRRYVALVHGLIPHEHGKVDAPIGRNPKDRQSMAVTRTNSKEAVTNFTVLKRYNAMSLIECRLETGRTHQIRVHMSYIGYPVYGDPKYGYR--KDDFSHGQFLHAKKLGFIHPTTQKYMEFESPLPDYFQ 293
>gi|167464425|ref|ZP_02329514.1| YlyB [Paenibacillus larvae subsp. larvae BRL-230010] (311 aa)
Score = 360, Expect = 2.0e-32, Identities = 100/289 (34%), Positives = 156/289 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKV-LTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +R+D  VS     +SR+  +  I+   ++VN K + KPN K+ E   I L    I +  +V + P    ++I YEDK +++VNKP  ++VHP     S TL N + Y    K +      +R GIVHR+DK T GL++ AK   +  +      +  + +KYLAL+  +L      V+API R     +     + ++KEA T F  + ++ ++TL E++L TGRTHQIRVH +FI + ++ DP YG     K    GQ L A  L F HP T++ +     +P++ K+ I
  S:    23 ERIDKFVSECLDGVSRTQIQQWIKEGHISVNEKQV-KPNYKLAEGDRIKLN---IPDPEQVDIRPEPIPLDIYYEDKDVIVVNKPRGMVVHPAPGHSSGTLVNALMY--HCKDLSGINGEMRPGIVHRIDKDTSGLIMAAKHDKAHASLADQLKEHSVTRKYLALVQGNLAHEQGTVEAPIGRDPKDRKLYTVTEKNSKEAVTHFVVMERFGDYTLTELKLETGRTHQIRVHMKFIGHPLVGDPAYGKS--KKEWIRGQALHAAVLGFKHPMTREYLEFEAPLPEDMKQLI 305
>gi|167040454|ref|YP_001663439.1| RluA family pseudouridine synthase [Thermoanaerobacter sp. X514] >gi|166854694|gb|ABY93103.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X514] (305 aa)
Score = 360, Expect = 2.0e-32, Identities = 97/290 (33%), Positives = 167/290 (57%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKV-LTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D+ ++++   +RS  K  I + LV VNGK + KP+ KV E  E+++    I E  K+ + P    ++I+YED  I+++NKP  ++VHP   + S TL N +  ++  K +      LR GIVHRLDK T G+++VAK+  +  + +    ++ + KKY+A++   ++    +++API R     R++++   D + A T++K + ++K  TL E  + TGRTHQIRVH  +I + ++ D +YG K   K    GQ L +  L F+HP     +     +P+ FK+ I+
  S:    18 KRIDVFLAAELDYTRSYIKKLIVDELVFVNGKTV-KPSYKVKENDEVVVN---IPEAEKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNAL--LYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKIEAPIGR-HPVDRKKMAVIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAYIGHPIVGDHVYGFKR-QKFKLEGQALHSSVLGFMHPTKGVYMEFEAPLPEYFKKLIE 300
>gi|116511823|ref|YP_809039.1| ribosomal large subunit pseudouridine synthase D [Lactococcus lactis subsp. cremoris SK11] >gi|116107477|gb|ABJ72617.1| ribosomal large subunit pseudouridine synthase D [Lactococcus lactis subsp. cremoris SK11] (301 aa)
Score = 359, Expect = 2.4e-32, Identities = 101/290 (34%), Positives = 159/290 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  ++++   SRS+    I+N+ V VN +   +K   K  +  E  + + ++++      P    +EI+YED  + +VNKP  ++VHP +   S TL N I Y I D   I  NG  +R GIVHR+DK T GL+++AK+  +  +      D+  +++YLA++H  L      ++API R     R++ +     K A T F+ + ++  +TL  + L TGRTHQIRVH  +I + V  DP+YGP     T   GQ+L A  L F HP + + +   +D P  FKE ++K
  S:    14 RLDKALANQTEYSRSLLTELIKNDKVFVNNEAKKAKYKVKTGDRIEFEIPQAEVLDVAAEDLP----LEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKDLSSI--NG-VIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGELANDKGTIEAPIGR-NLKDRKKQAVVSGGKPAVTHFEVLERFVGYTLIALRLETGRTHQIRVHMHYIGHPVAGDPLYGPNK-TLTPNKGQFLHAETLGFEHPTSGELMEFQVDAPDLFKEQLEK 296
>gi|163941632|ref|YP_001646516.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis KBAB4] >gi|163863829|gb|ABY44888.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis KBAB4] (302 aa)
Score = 358, Expect = 2.7e-32, Identities = 104/290 (35%), Positives = 161/290 (55%)
  Q:     2 KNTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           + ++R+D  V+   S  SRS  +  I++ +VTVNGK + K N KV    EI +   +   E   + P   ++E+ YED  +L+VNKP  ++VHP       TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK        GQ L A  L F HP T + +     +P+ F+E
  S:    13 QKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSV-KGNYKVKGNDEITVTIPE--PEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGIIDAPIGR-DKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDMN--GQALHAGILGFDHPRTGEYIEFEAPIPEVFEE 295
>gi|167037761|ref|YP_001665339.1| RluA family pseudouridine synthase [Thermoanaerobacter pseudethanolicus ATCC 33223] >gi|166856595|gb|ABY95003.1| pseudouridine synthase, RluA family [Thermoanaerobacter pseudethanolicus ATCC 33223] (305 aa)
Score = 358, Expect = 3.0e-32, Identities = 97/290 (33%), Positives = 165/290 (56%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D+ ++++   +RS  K  I + LV VNGK + KP+ KV E  E++L   +  E+  VL P    ++I+YED  I+++NKP  ++VHP   + S TL N +  ++  K +      LR GIVHRLDK T G+++VAK+  +  + +    ++ + KKY+A++   ++    +++API R     R++++   D + A T++K + ++K  TL E  + TGRTHQIRVH  +I + ++ D +YG K   K    GQ L +  L F+HP     +     +P+ F   I+
  S:    18 KRIDVFLAAELDYTRSYIKKLIVDGLVFVNGKTV-KPSYKVKENDEVVLNVPE-AEKIDVL-PEDIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNAL--LYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKIEAPIGR-HPVDRKKMAVIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAYIGHPIVGDHVYGFKR-QKFKLEGQALHSSVLGFMHPTKGVYMEFEAPLPEYFVRLIE 300
>gi|167758164|ref|ZP_02430291.1| hypothetical protein CLOSCI_00502 [Clostridium scindens ATCC 35704] >gi|167664061|gb|EDS08191.1| hypothetical protein CLOSCI_00502 [Clostridium scindens ATCC 35704] (304 aa)
Score = 358, Expect = 3.1e-32, Identities = 99/297 (33%), Positives = 160/297 (53%)
  Q:     2 KNTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           ++ +R+D  +S + +  SRS  +  I+ N VTVN K + K N ++   +  EI L E K  +    + P    ++I+YEDK I+IVNKP  ++VHP     S TL N + Y   S     NG  +R GIVHR+D  T G ++  K+  +  + ++   +  I + Y+A++H +++     V+API R  T  ++      + +EA T ++ + ++ ++T    EL TGRTHQIRVH   + + ++ D +YGPK        GQ L A  L  IHP T + + +N  +P  F E + K  K
  S:    10 QDGERIDRYLSEELADRSRSYIQKLIKENYVTVNQKPV-KANYRLSLGDRVEIDLPEAKEPD----IRPEDIPLDILYEDKDIIIVNKPKQMVVHPAPGHYSQTLVNALMYHCGSDLSGINGT-MRPGIVHRIDMDTTGSLVACKNDMAHQSLSRQLKEHSIRRIYVAIVHGNIKEEYGTVNAPIGRHPTERKKMSIHSRNGREAVTHYQVLERFGDYTYIRCELETGRTHQIRVHMASLGHPLLGDGVYGPKKCPFPPLQGQTLHARTLGIIHPRTGEYLEVNAPLPAYFIELLDKLRK 303
>gi|73662884|ref|YP_301665.1| putative pseudouridylate synthase [Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305] >gi|72495399|dbj|BAE18720.1| putative pseudouridylate synthase [Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305] (305 aa)
Score = 358, Expect = 3.4e-32, Identities = 102/291 (35%), Positives = 163/291 (56%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           QR+D L+    S  SR+  +  I+ +LV VN ++I K N K      I++ E++ VE    + P   +++I YED  + IV KP  ++VHP++   + TL N + Y    K +      +R GIVHR+DK T GL++VAK+  +  +     +++ + +KY+AL+H  +      VDAPI R   + R+ +    D KEA T F  +  +  +TL E +L TGRTHQIRVH ++I   ++ DP YGPK   KT    GQ L A  + F HP T + +  +  +P++F++ + +
  S:    16 QRIDKLLPEYHSEWSRTQIQDWIKASLVKVNDQVI-KSNYKTKMNDHIVVTEKETVEAD--IQPENLNLDIYYEDDDVAIVYKPKGMVVHPSAGHYTGTLVNGLMY--QMKNLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVDQLVNKTVTRKYVALVHGKIPHDYGTVDAPIGR-NKNDRQSMDVVDDGKEAVTHFNVLEHFNKYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPK---KTLDIGGQALHAGIIGFEHPVTHEYIEKSTALPEDFEQLLSE 299
>gi|85860531|ref|YP_462733.1| ribosomal large subunit pseudouridine synthase D [Syntrophus aciditrophicus SB] >gi|85723622|gb|ABC78565.1| ribosomal large subunit pseudouridine synthase D [Syntrophus aciditrophicus SB] (333 aa)
Score = 357, Expect = 3.9e-32, Identities = 92/286 (32%), Positives = 155/286 (54%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-----------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           RLD+ ++S  S  SR+  +  IE+  VT++GK   + + K+    +I++ EE      + L P    + I+YED  +L+++KP  ++VHP +  +S TL N +  +F  + +   G  +R GIVHRLDK T GL++VAK+  +       F   ++ K Y AL++   + +T ++D P+ R     ++  ++    KEA T ++   ++   TL  V++ TGRTHQIRVH   I + V+ D +YG      T               Q L A +L F HP T K +  +  +P + ++
  S:    20 RLDLFLASHESGFSRARLQRLIESGRVTISGKAAIRASQKL-RTGDIVMLEEPPATPLE-LIPQDIPLSILYEDHDLLVLDKPAGLVVHPAAGHVSGTLVNAL--LFHCRDLAGIGGVMRPGIVHRLDKDTSGLLVVAKTDAAHQGLALQFKKHQVGKTYQALVYGDPREKTGQIDLPVGRHPVERKKMSTKSRRGKEAATRWRIAERFGVATLLNVDIVTGRTHQIRVHLAAIGHPVVGDAVYGSSKRATTLTDPAVKGRLKEMSRQALHAARLSFTHPVTHKILEFHAPLPADMED 313
>gi|154685962|ref|YP_001421123.1| YlyB [Bacillus amyloliquefaciens FZB42] >gi|154351813|gb|ABS73892.1| YlyB [Bacillus amyloliquefaciens FZB42] (304 aa)
Score = 357, Expect = 4.0e-32, Identities = 102/293 (34%), Positives = 167/293 (56%)
  Q:     2 KNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           + ++R+D  L S+  + SR+  +  ++  LV+VNGK + K N K+   ++  + + E    EE  VL     D++I YED+ +L+VNKP  ++VHP    ++ TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     +++ + +KY A++H  +      +DAPI R +   +        +K A T F  + ++++FTL E  L TGRTHQIRVH ++I   +  DP YGP+   KT  + GQ L A  L F HP T + +     +P++ K+ I+
  S:    12 QKSERIDKFLASTGENWSRTQVQQWVKEGLVSVNGKSV-KANYKMQPGDQVNVTIPEP---EELDVLAE-PMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNGLMAHCNDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGVISHDDGTIDAPIGRDKKDRQSMTVTRESSKNAVTHFHVLERFQDFTLVECRLETGRTHQIRVHMKYIGFPLAGDPKYGPR---KTIDFNGQALHAGILGFDHPRTGEYMEFEAPLPEDMKKLIE 298
>gi|56551646|ref|YP_162485.1| pseudouridine synthase D large subunit [Zymomonas mobilis subsp. mobilis ZM4] >gi|59803028|sp|P50513|RLUD_ZYMMO Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|56543220|gb|AAV89374.1| pseudouridine synthase D large subunit [Zymomonas mobilis subsp. mobilis ZM4] (317 aa)
Score = 356, Expect = 4.8e-32, Identities = 83/228 (36%), Positives = 128/228 (56%)
  Q:    67 PWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRR-EVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKH------INKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           P    +EIV+ED+++L+VNKP  ++VHP + +  NTL N + Y   + K+   G   R GIVHR+DK T GL++VAK+  +       F D  I ++Y A++  H   +   VDAP+ R   + ++  +  D   K A T ++ I   KN +L E  L TGRTHQ+RVH   I + ++ DP+YG         +       Q L A  L FIHP + K+V+ + +MP++ +   K
  S:    77 PQDIPLEIVFEDEHLLVVNKPAGMVVHPAAGNYDNTLVNALLY-HCAGKLSGIGGVARPGIVHRIDKDTSGLLVVAKTDPAHAGLAAQFADHSINRRYRAIVDGHPSLQG-HVDAPLARSSVNRQKMAIVSDGRGKRAVTHYRMITPLKNASLIECRLETGRTHQVRVHMSSIGHSLLGDPVYGRSKKAHHALLQSLAFQRQALHAAHLGFIHPISGKQVDFDAEMPQDMQLLFK 309
>gi|31544413|ref|NP_852991.1| hypothetical protein MGA_0996 [Mycoplasma gallisepticum R] >gi|31541257|gb|AAP56559.1| RluA [Mycoplasma gallisepticum R] (312 aa)
Score = 356, Expect = 5.0e-32, Identities = 100/285 (35%), Positives = 166/285 (58%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPN--TKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRR-EVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHP---------------FTQKEVNINLDMPKEFK 290
           RLDI ++   +LSR+     I N+LV VN K+++K N   KV +  E+  +E    + +  + P+ K ++IVYED  ++IVNKP +++ HPT+++  +TL N + Y    +K+          + HRLDK T GL++  K+  +     +    + +++ YLA++H         +DAPI  ++    +  V    + K A T    +++ K + L + EL TGRTHQIRVH +FIK+++INDP+YG K   + T Y Q+L AY+L+  HP               F +K  +++LD+ +E K
  S:    16 RLDIFLTYNLNLSRNKTSFLILNDLVKVNKKLVNKNNFVLKVGDVVELEYEESIFNKVSNEILPFNKKLDIVYEDDDLIIVNKPTNMLSHPTTHNEPDTLLNCLMYHNKKQKVY---------LAHRLDKDTTGLIVATKNFKALEKIQEQITKRIMKRYYLAIVHYPFNELRAVIDAPIGYLKDHDLKFGVENTKNPKNAITKIYVLDQNKKYALIKCELLTGRTHQIRVHMDFIKHNIINDPLYGVKG-EQRTDYKQFLHAYQLELTHPTTNVSLFFEVKPDEVFMKKLFDVHLDLNQELK 308
>gi|125624328|ref|YP_001032811.1| ribosomal large subunit pseudouridine synthase D [Lactococcus lactis subsp. cremoris MG1363] >gi|124493136|emb|CAL98100.1| ribosomal large subunit pseudouridine synthase D [Lactococcus lactis subsp. cremoris MG1363] (301 aa)
Score = 356, Expect = 5.3e-32, Identities = 104/290 (35%), Positives = 158/290 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  ++++   SRS+    I+N+ V VN +   K   KV     I  +    + + +VL    +D+  EI+YED  + +VNKP  ++VHP +   S TL N I Y I D   I  NG  +R GIVHR+DK T GL+++AK+  +  +      D+  +++YLA++H  L      ++API R     R++ +     K A T F+ +  +  +TL  + L TGRTHQIRVH  +I + V  DP+YGP     T   GQ+L A  L F HP + + +   +D P  FKE ++K
  S:    14 RLDKALANQTEYSRSLLTELIKNDKVFVNNEA-KKAKYKVKTGDRIQFE----IPQAEVLDVVAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKDLSSI--NG-VIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGELANDKGTIEAPIGR-NLKDRKKQAVVSGGKPAVTHFEVLEGFVGYTLIALRLETGRTHQIRVHMHYIGHPVAGDPLYGPNK-TLTPNKGQFLHAETLGFEHPTSGELMEFQVDAPDLFKEQLEK 296
>gi|39938617|ref|NP_950383.1| pseudouridylate synthase [Onion yellows phytoplasma OY-M] >gi|39721726|dbj|BAD04216.1| pseudouridylate synthases [Onion yellows phytoplasma OY-M] (303 aa)
Score = 356, Expect = 5.3e-32, Identities = 99/290 (34%), Positives = 154/290 (53%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNT-KVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  + +  +L++S  +  I    V VN K   K    K  +   +I+ + +  E   + TP   +++I+YED Y+ ++NKP +++ HP+      TL N + Y F +     + D  R GIVHRLDK T GL+I+AK+ D  +     F  +KI K Y AL+   L+ +   +  PI R     R ++    D K A T FK + ++ +F+L E  L TGRTHQ+R H  F+K  +I D +YG  H    T  GQ+L A  LKF HP T + + +   +P  F++ ++
  S:    16 QRLDHFLLTHINLNKSQCQKLILAQQVLVNSKPAKKSYLLKAQDLITVIIPQTQ--ESVNLQTPQNLNLDIIYEDPYLAVINKPANLVAHPSLSFQETTLVNGLLYQFATLS---HVDTQRPGIVHRLDKNTTGLLIIAKNNDVSDKLQIAFQQRKITKIYWALIEGFLEDKGT-IKLPIGR-NPHNRLKMQVIPDGKTAVTHFKTLQRFSHFSLMEFNLETGRTHQLRAHFSFLKRPIIGDLLYGSSH--HITPLGQFLHAKMLKFNHPITNQNLILEAPLPANFEKLLQ 297
>gi|58337436|ref|YP_194021.1| pseudouridine synthase [Lactobacillus acidophilus NCFM] >gi|58254753|gb|AAV42990.1| pseudouridine synthase [Lactobacillus acidophilus NCFM] (302 aa)
Score = 355, Expect = 6.4e-32, Identities = 98/288 (34%), Positives = 166/288 (57%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD  +S + S LSR+  K  I++  + VN K+  K + K+ +  +I    E  V   K L    ++I  +IVYED  +++VNKP  ++VHP      +TL N +  ++ ++ +  + +  R GIVHR+DK T GL+++AK+  +  +  +   ++  ++ Y A++H +       +DAPI R     R++++   + K+A T FK + ++K ++L E +L TGRTHQIRVH ++I + V  DP+YGP+   K    GQ+L A  L F HP T K +  +++ PK F+  +
  S:    15 RLDKFISEQLSDLSRTRVKELIQDQNILVNEKV-EKVSYKIQDGDKI----EITVPAVKPLDIVAENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNAL--LYHTQDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNATARESLEQQLANKTNKRIYWAIVHGNFSEEQGSIDAPIGR-NPYDRKKMAVVENGKKAITHFKVLKQFKGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGN--GQFLHAKILGFKHPKTGKWLEFSVEPPKIFQNML 295
>gi|118727641|ref|ZP_01576235.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum H10] >gi|118662972|gb|EAV69639.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum H10] (304 aa)
Score = 355, Expect = 7.7e-32, Identities = 95/278 (34%), Positives = 159/278 (57%)
  Q:    18 SRSIAKHKIENNLVTVNG-KIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           SRS  +    +  V  NG ++ S    K D+  ++ + E +I++    + P    ++IVYEDK+I+++NKP  ++VHP   + + TL N ++K+  DS     NG  +R GIVHR+DK T GL++VAKS  +    ++      I+++Y+AL+   +   + ++DAPI R     ++      + + A T FK + +++N T  E++L TGRTHQIRVH  +I + +I D +YG +     TK GQ L A++L F HP T +EV     +P+ F+  + +
  S:    27 SRSYIQKLCLDGNVWANGIQVKSNYRVKTDDNIKVNVPEAEILD----VEPEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNYTGTLVNALMKHCGDSLS-DING-VIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDIKREYIALVDGIIYENSGKIDAPIGRNPVERKKMCVNTENGRNAITHFKVLERFQNATYLELKLETGRTHQIRVHMAYINHPIIGDMVYGRRKQKYKTK-GQVLHAWRLSFQHPITGEEVKFETAVPEYFQRILSQ 299
>gi|52080148|ref|YP_078939.1| pseudouridine synthase [Bacillus licheniformis ATCC 14580] >gi|52785525|ref|YP_091354.1| YlyB [Bacillus licheniformis ATCC 14580] >gi|52003359|gb|AAU23301.1| Pseudouridine synthase [Bacillus licheniformis ATCC 14580] >gi|52348027|gb|AAU40661.1| YlyB [Bacillus licheniformis DSM 13] (304 aa)
Score = 354, Expect = 7.9e-32, Identities = 103/291 (35%), Positives = 160/291 (54%)
  Q:     5 QRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  L + +   SR+  +  I+ + V VNG  + K N KV E   + ++  +   E   +T    D++I YED+ +L+VNKP  ++VHP    L+ TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     +++ + +KY AL+H  +      +DAPI R +   +       + K A T F+ I ++ +FT+ E +L TGRTHQIRVH ++I   +  DP YGPK   KT  + GQ L A  L F HP T + V     +P + K  + K
  S:    15 ERIDKYLTAVEADWSRTQVQQWIKEDRVLVNGNAV-KANYKVQEGDAVSVQVPE--PEPLDVTAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCDDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTALVHGVIPHDHGTIDAPIGRDKKDRQSMTVTRENGKHAVTHFEVIERFDDFTVVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPK---KTVDFNGQVLHAGVLGFDHPRTGEYVEFEAPLPDDMKNLLDK 299
>gi|15672980|ref|NP_267154.1| ribosomal large subunit pseudouridine synthase D [Lactococcus lactis subsp. lactis Il1403] >gi|12723945|gb|AAK05096.1|AE006334_2 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403] (301 aa)
Score = 354, Expect = 8.1e-32, Identities = 102/290 (35%), Positives = 157/290 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  ++++   SRS+    I+N+ V VN +           +     + E  V E +VL    +D+  EI+YED  + +VNKP  ++VHP +   S TL N I Y I D   I  NG  +R GIVHR+DK T GL+++AK+  +  +      D+  +++YLA++H  +      ++API R     R++ +     K A T F+ + ++  +TL  + L TGRTHQIRVH  +I + V  DP+YGP     T   GQ+L A  L F HP T + +   +D P+ F E ++K
  S:    14 RLDKALANQTEYSRSLLTELIKNDKVFVNSEAKKAKYKVKVGD-----RIEFEVPEAEVLDIVAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKDLSSI--NG-VIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGEIANDKGTIEAPIGR-NLKDRKKQAVVSGGKPAVTHFEVLERFYGYTLIALRLETGRTHQIRVHMNYIGHPVAGDPLYGPNK-TLTPNKGQFLHAETLGFDHPTTGEFMEFQVDAPEIFNEQLEK 296
>gi|28378455|ref|NP_785347.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1] >gi|28271291|emb|CAD64195.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1] (307 aa)
Score = 354, Expect = 8.7e-32, Identities = 101/295 (34%), Positives = 162/295 (54%)
  Q:     4 TQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK-YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           T RLD +L + +   +RS     I+ + VTVNG++       V    EI++  + + + T  + P    ++IVYED  +L+VNKP  ++VHP     ++TL N +  ++ S     NG+  R GIVHR+DK T GL++VAK+  +  +       +   ++Y+AL+H  ++  T  ++AP+ R     R++ +     + A T FK + +Y+++TL    L TGRTHQIRVH + I + ++ DP+YGPK   KT K +GQ+L A  L F HP T   +     +P  F   + K  K
  S:    16 TGRLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQL-EASKYHVKPGDEIVVAAQTVQQTT--IEPENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNAL--LYHSPLSTINGE-FRPGIVHRIDKDTSGLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKEDTGTINAPLGR-SPKDRKKQAIVKTGRPAVTHFKVLKRYQHYTLISCRLETGRTHQIRVHLQSIGHPLVGDPLYGPK---KTIKGHGQFLHAKLLGFKHPVTGDLLTFEAPLPPIFTTTLAKLDK 302
>gi|169827034|ref|YP_001697192.1| putative RNA pseudouridine synthase ylyB [Lysinibacillus sphaericus C3-41] >gi|168991522|gb|ACA39062.1| Hypothetical RNA pseudouridine synthase ylyB [Lysinibacillus sphaericus C3-41] (303 aa)
Score = 354, Expect = 9.6e-32, Identities = 96/291 (32%), Positives = 160/291 (54%)
  Q:     5 QRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  +SS +   SR+   + I +  + VNG  + K   KV +  ++I  +    E   V+      ++IVYED  +L+VNKP  ++VHP    ++ TL N + Y    K +      +R GIVHR+DK T GL++VAK+  +  +     +++ + +KY+AL+H H+      +DAPI R +   +++   D + K A T F  + ++ ++TL E  L TGRTHQIRVH  +I   ++ DP YGPK   KT  + GQ L A  L F HP + + +     +P ++++ + +
  S:    15 ERIDKALSSLQSEWSRTQIGNWISDGNIKVNGDAV-KAKYKV-KAGDVIAIDVPEAEPLDVIAE-NLALDIVYEDADVLVVNKPKGMVVHPAPGHMTGTLVNGLMY--QCKDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNKTVTRKYIALVHGHIAHDKGTIDAPIGRDQKDRQKQAIVD-NGKHAVTHFHVVERFGDYTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPK---KTIDFGGQVLHAATLGFNHPSSGEYLEFETPLPADYEQLLNE 298
>gi|163764829|ref|ZP_02171882.1| protoheme IX farnesyltransferase [Bacillus selenitireducens MLS10] >gi|160354723|gb|EDP81383.1| protoheme IX farnesyltransferase [Bacillus selenitireducens MLS10] (307 aa)
Score = 354, Expect = 9.7e-32, Identities = 94/278 (33%), Positives = 153/278 (55%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           SRS+ +  I+   VTVN +  SK N K+ +  +++  +   VEE ++ T    D++IVYED+ +++VNKP  ++VHP     S TL N + Y    + +       R GIVHR+DK T GL++VAK   +  +      ++   ++Y AL+   +      VDAPI R     ++    + +A++A T F+ I +   +T    EL TGRTHQIRVH ++I   ++ DP YGP+  +  +  GQ L A  L F+HP T +++    ++P+ FKE + +
  S:    27 SRSLTQSWIQEGYVTVNDET-SKANYKL-KIGDVVRVKVPEVEELEI-TAEDLDLDIVYEDQDVIVVNKPAGMVVHPAPGHPSGTLVNGLMY--HCQDLSGINGVARPGIVHRIDKDTSGLLMVAKHDKAHESLVDQLKNKTTIRQYEALVVGTIPHEKGTVDAPIGRDPQDRQKMTVTEENARDAVTHFQVIERMNGYTHVLCELETGRTHQIRVHMKYIGYPIVGDPKYGPRKKHDFSIEGQALHARTLGFVHPVTGEQMTFEAEVPERFKETLDQ 299
>gi|158522832|ref|YP_001530702.1| RluA family pseudouridine synthase [Desulfococcus oleovorans Hxd3] >gi|158511658|gb|ABW68625.1| pseudouridine synthase, RluA family [Desulfococcus oleovorans Hxd3] (329 aa)
Score = 354, Expect = 9.8e-32, Identities = 92/288 (31%), Positives = 153/288 (53%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG-------------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD LV+ ++  SR  A   I+N  + V+G+   KP+ KV     I  +     ++ +   P    + +++ED ++L+VNKP  ++VHP       TL N + + F +  I   G+P R GIVHRLD+ T G ++VAK+  +  A + +F  +++ K YLAL++  +++    V  PI R     ++       A+ A T +K    + + +L E+E+ TGRTHQIRVH   ++  V+ DP Y  K   K   +              Q L A++L+F HP T   +     + ++ KE +
  S:    19 RLDTLVAGQWDCSRHSAALLIKNGTILVDGRP-QKPSYKVGVNQSITGRIPS--QKPEKPGPEPAPLPLLFEDAFLLVVNKPPGLVVHPAPGHEGGTLVNRLLHHFPA--IGTVGEPDRPGIVHRLDRNTSGALVVAKTAAAHQALSDMFKSRQVRKTYLALVYGQMKSTGGVVTLPIGRHSLERKKMSVSSPQARPAETRWKVRKAFVDASLLELEIHTGRTHQIRVHCTALQRPVVGDPTYPCKWTRKRQHFSSRASFELLNAAGRQMLHAWRLEFDHPVTGAPMCFTAPLFEDIKEML 314
>gi|170759197|ref|YP_001786899.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str. Loch Maree] >gi|169406186|gb|ACA54597.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str. Loch Maree] (305 aa)
Score = 353, Expect = 1.1e-31, Identities = 105/289 (36%), Positives = 158/289 (54%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKP-NTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ +S  F   SRS  +  I+   V VN K   +    KV +  EI + E K+++    + P    ++++YEDK +++VNKP +++VHP     S TL N +  +   K +       R GIVHR+DK T G+++VAK+  S N     F +  I + Y+AL+   ++     ++API R     R +++   D + A T +K I ++KN TL E  L TGRTHQIRVH   I + ++ DP+YG K      K GQ L A  L FIHP T + V    ++P+ FK+ IK
  S:    16 RLDLCLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIEINIPEPKLLQ----IEPEDVKLDVIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNAL--LHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKNEQGTIEAPIGR-HPVDRIKMAVVKDGRHAVTHYKVIKRFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLK-GQMLHAKLLGFIHPTTGQYVEFESELPEYFKKIIK 298
>gi|168180134|ref|ZP_02614798.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC 2916] >gi|182669142|gb|EDT81118.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC 2916] (305 aa)
Score = 353, Expect = 1.2e-31, Identities = 105/289 (36%), Positives = 160/289 (55%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKP-NTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ +S  F   SRS  +  I+   V VN K   +    KV +  E+ + E K+++    + P   +++I+YEDK +++VNKP +++VHP     S TL N +  +   K +       R GIVHR+DK T G+++VAK+  S N     F +  I + Y+AL+   ++     ++API R     R +++   D + A T +K I ++KN TL E  L TGRTHQIRVH   I + ++ DP+YG K      K GQ L A  L FIHP T++ V    ++P+ FK+ IK
  S:    16 RLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVRDNIEVNIPEPKLLQ----IEPEDINLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNAL--LHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQGTIEAPIGR-HPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLK-GQMLHAKLLGFIHPTTRQYVEFESELPEYFKKIIK 298
>gi|166367953|ref|YP_001660226.1| ribosomal large subunit pseudouridine synthase D [Microcystis aeruginosa NIES-843] >gi|166090326|dbj|BAG05034.1| ribosomal large subunit pseudouridine synthase D [Microcystis aeruginosa NIES-843] (308 aa)
Score = 352, Expect = 1.3e-31, Identities = 92/289 (31%), Positives = 154/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEES--EIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRRE--VSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +RLD  + S    LSRS  +  IE   + +NG+I +  NTKV +    +I + + + +E    LT    +++I+YED Y++I+NKP D++VHP     S TL N +  +     +   G   R GIVHRLDK T G +++AK+  +          +   ++Y+AL+H   ++ T  +D PI R  +  ++   ++ +   + A T ++   +  N+TL E  L TGRTHQIRVH+  I + ++ DP+Y           GQ L A++L  +HP T + +     +P  F + +
  S:    13 ERLDAWMGSHLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQGDRLKITIPDSQPLE----LTAEAIELDILYEDDYLIIINKPADLVVHPAPGHESGTLVNAL--LHHCPNLAGIGGIQRPGIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYIALVHGVPKSETGTIDLPIGRHRSDRQKMAIIAVEKGGRNAVTHWQVKERLGNYTLMEFRLETGRTHQIRVHSSHIGHPILGDPLYSSGRSIGINLPGQLLHAHRLILVHPVTGESLEAIAPLPAIFPKVL 300
>gi|168700598|ref|ZP_02732875.1| ribosomal large subunit pseudouridine synthase [Gemmata obscuriglobus UQM 2246] (354 aa)
Score = 352, Expect = 1.6e-31, Identities = 89/273 (32%), Positives = 153/273 (56%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIK-RVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG--------------QYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           SRS+ +  IE+  V +NG+ + KP+ KV +   + +   +   E  V  P    ++I+Y+D+++ +VNKP D++VHP   + S TL N +++ F  + +      LR GIVHRLDK T G+++VAK   +       F  +K+ K+Y+A+    L+  +  ++  +K       +  VS D DAK A + ++ + +++ FTL +V+  TGRTHQIRVH   +   V+ D IYG +   K ++                Q L A++L+F HP T + +     +P + +
  S:    57 SRSVVQRAIESGGVLLNGRPVLKPSYKVRKNDRLHVTMPEPTHEIPV--PEDIPLDILYQDEWLALVNKPADMVVHPAKGNWSGTLVNALQWHF-REHLSTGAGHLRAGIVHRLDKDTSGVILVAKDDLTHRDLAMQFESRKVFKEYVAIAAGELERDSDYIEGALKMHPYDRLKMIVSTDPDAKHALSYYEVLERFRGFTLVKVQPRTGRTHQIRVHLLHVGCAVLADKIYGGRAQVKLSEIAPGTPPAEDEVLLGRQALHAFRLRFQHPRTGQWIEAEAPLPPDMR 341
>gi|148379448|ref|YP_001253989.1| pseudouridine synthase, RluA family [Clostridium botulinum A str. ATCC 3502] >gi|153934249|ref|YP_001383827.1| RluA family pseudouridine synthase [Clostridium botulinum A str. ATCC 19397] >gi|153935171|ref|YP_001387377.1| RluA family pseudouridine synthase [Clostridium botulinum A str. Hall] >gi|148288932|emb|CAL83019.1| putative ribosomal large subunit pseudouridine synthase [Clostridium botulinum A str. ATCC 3502] >gi|152930293|gb|ABS35793.1| pseudouridine synthase, RluA family [Clostridium botulinum A str. ATCC 19397] >gi|152931085|gb|ABS36584.1| pseudouridine synthase, RluA family [Clostridium botulinum A str. Hall] (305 aa)
Score = 352, Expect = 1.6e-31, Identities = 105/289 (36%), Positives = 159/289 (55%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKP-NTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ +S  F   SRS  +  I+   V VN K   +    KV +  E+ + E K+++    + P    ++I+YEDK +++VNKP +++VHP     S TL N +  +   K +       R GIVHR+DK T G+++VAK+  S N     F +  I + Y+AL+   ++     ++API R     R +++   D + A T +K I ++KN TL E  L TGRTHQIRVH   I + ++ DP+YG K      K GQ L A  L FIHP T++ V    ++P+ FK+ IK
  S:    16 RLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIEVNIPEPKLLQ----IEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNAL--LHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQGTIEAPIGR-HPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLK-GQMLHAKLLGFIHPTTRQYVEFESELPEYFKKIIK 298
>gi|171853861|emb|CAM11823.1| Pseudouridine synthase [Candidatus Phytoplasma australiense] (302 aa)
Score = 352, Expect = 1.6e-31, Identities = 98/291 (33%), Positives = 158/291 (54%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           QRLD  + S+ + ++S  +  I    V VN K  +K N  +  +  I +          +  P+  ++E+VYED  + ++NKP+++IVHP+      TL N + + F S     N D  R GIVHRLDK T GL+++AK+ ++       F  + I+K Y  L+   L+     ++ PI R   + R +++   + KEA T FK + +  NF+L +  L TGRTHQIR H  ++K  ++ D +YG KH N  T  GQ+L A +L F HP + +E+N+   +P  F++ + K
  S:    16 QRLDHFLVSQTTWNKSQCQKLIAAKKVLVNQKP-TKKNYLLKNQDLITIPTTVFKTPLNIQKPYNLNLEVVYEDSDLAVINKPSNLIVHPSLSFEGITLVNALLHQFSSLS---NIDTPRPGIVHRLDKNTTGLMLIAKNDNTSQKLQTAFSQRTIKKVYWGLIEGFLENEGT-INLPIAR-NPNDRLKMTVLPNGKEAVTHFKTLKRLNNFSLMQFVLETGRTHQIRAHLSYLKKPLLGDKLYGSKHYN--TDEGQFLHAKELIFKHPISFQEINLQAPLPLNFQKLLDK 298
>gi|160938833|ref|ZP_02086184.1| hypothetical protein CLOBOL_03727 [Clostridium bolteae ATCC BAA-613] >gi|158437796|gb|EDP15556.1| hypothetical protein CLOBOL_03727 [Clostridium bolteae ATCC BAA-613] (294 aa)
Score = 352, Expect = 1.7e-31, Identities = 94/294 (31%), Positives = 159/294 (54%)
  Q:     1 MKNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           M++  R+D  L  +   LSRS  +  +++  V VNG+ I K +  V E+  I L+  + VE      P   D++I+YED+ ++++NKP  ++VHP +   S+TL N + Y    +    NG  +R GIVHR+D  T G++I  K+  + ++      +  I ++Y A++H  +      VDAPI R     ++      + K A T ++ +N+++ +T  E  L TGRTHQIRVH   I++ ++ D +YGP     +   GQ L A  L FIHP T + +  +  +P  F++ ++
  S:     1 MEDHVRIDKYLAEACPDLSRSYIQKLLKSGQVLVNGQGI-KASYIVVEDDRIELEVPEAVEPEIDAEP--MDLDILYEDQDLILINKPKGMVVHPAAGHYSHTLVNGLMYHCKDQLSGING-VMRPGIVHRIDMDTTGVIIACKNDMAHSSIAAQLKEHSITRRYQAIVHGVIAEDEGTVDAPIGRHPVERKKMSINYQNGKNAVTHYRVLNRFRQYTHVECRLETGRTHQIRVHMASIRHPLLGDAVYGPARCPISGLCGQTLHAGILGFIHPRTGEYMEFSAPLPDYFEKLLR 291
>gi|153940691|ref|YP_001390824.1| RluA family pseudouridine synthase [Clostridium botulinum F str. Langeland] >gi|152936587|gb|ABS42085.1| pseudouridine synthase, RluA family [Clostridium botulinum F str. Langeland] (305 aa)
Score = 351, Expect = 1.8e-31, Identities = 105/289 (36%), Positives = 159/289 (55%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKP-NTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ +S  F   SRS  +  I+   V VN K   +    KV +  E+ + E K+++    + P    ++I+YEDK +++VNKP +++VHP     S TL N +  +   K +       R GIVHR+DK T G+++VAK+  S N     F +  I + Y+AL+   ++     ++API R     R +++   D + A T +K I ++KN TL E  L TGRTHQIRVH   I + ++ DP+YG K      K GQ L A  L FIHP T++ V    ++P+ FK+ IK
  S:    16 RLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIEVNIPEPKLLQ----IEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNAL--LHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKYEQGTIEAPIGR-HPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLK-GQMLHAKLLGFIHPTTRQYVEFESELPEYFKKIIK 298
>gi|163782801|ref|ZP_02177797.1| hypothetical protein HG1285_15736 [Hydrogenivirga sp. 128-5-R1-1] >gi|159881922|gb|EDP75430.1| hypothetical protein HG1285_15736 [Hydrogenivirga sp. 128-5-R1-1] (322 aa)
Score = 351, Expect = 1.9e-31, Identities = 98/291 (33%), Positives = 157/291 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYK--NFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG------PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +RLD  ++  +  LSRS  K  IE     V GK+  KP+ +V E   + L   +   E   + P    IE+VYED+ ++++ KP  ++VHP+    S TL N +  ++  K +   G   R GIVHRLDK T GL++VAK+  S     + F  ++ EK Y AL+   ++     ++ PI R     ++  +    +K A++ F  + ++     TL +V+++TGRTHQIRVH   I + ++ D  YG      P+ IN+       LVAYKL F HP + + +   +D P+ F   +K+
  S:    19 ERLDTFLAKAYPELSRSYIKRLIEEGFALVEGKV-RKPSYRVKEGDRVTLSVPE--PEPLEVKPEDIPIEVVYEDRDVVVIVKPCGLVVHPSPGYTSGTLVNAL--LYHIKDLSSIGGVERPGIVHRLDKETAGLMVVAKNDTSHRNLVEQFASRRTEKLYRALVKGTVKEEHGILELPIGRHPFHRKKFSTSSPRSKPAKSEFWVLERFPGLELTLLKVKIYTGRTHQIRVHLSSIGHPIVGDTTYGFKRSSVPEAINRLLGECNMLVAYKLGFYHPSSGRWLEFEIDDPEPFGSVLKE 313
>gi|171326689|ref|ZP_02915137.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70] >gi|171087318|gb|EDT33729.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70] (304 aa)
Score = 351, Expect = 2.1e-31, Identities = 98/292 (33%), Positives = 162/292 (55%)
  Q:     3 NTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           + +R+D ++++     SRS  +  I++ LVTVN + + K N K      ++++  +   E   + P    ++I YED  +L+VNKP  ++VHP    +  TL N ++ +  D   I  NG  LR GIVHR+DK T GL++VAK+  +  +     + + + +KY A++H  +      +DAPI R +   ++    + + KEA T F+ + +++++T  E +L TGRTHQIRVH ++I   +  DP YGPK   KT    GQ L A  L F HP T + +     +P EF+  ++
  S:    13 DNERIDKVIAALNEEWSRSKVQQWIKDGLVTVNDQHV-KANYKSSAGDVVVVRLPE--PEPLHVVPENIPLDIYYEDADVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCTDLSGI--NG-VLRPGIVHRIDKDTSGLLMVAKNDMAHQSLVDQLVKKTVTRKYKAIVHGVIPHDYGTIDAPIGRDKRDRKKMTVTEENGKEAVTHFRVLERFRHYTFVECQLETGRTHQIRVHMKYIGYPLAGDPQYGPK---KTLPIDGQALHAGVLGFTHPRTGEYLEFEAPLPPEFEHLLQ 298
>gi|71894605|ref|YP_278713.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma synoviae 53] >gi|71851393|gb|AAZ44002.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma synoviae 53] (303 aa)
Score = 351, Expect = 2.1e-31, Identities = 101/284 (35%), Positives = 160/284 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTT-KYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           R+D  ++S  SLSR+  +  I++  V VN  ++ KP+  V    EI  K  +++++T  +      ++I+YED +++I++KP+ +IVHP+     NTLAN + Y F +     NG  LR GIVHR+DK T GL+IV K+        ++F +  I++ Y+A+  N L  + + ++ PI     + ++    +I AKEA T  + I  +    +  +L +  L TGRTHQIRVH        IN+PIYG    NK    + Q L AYKL+F HP  +K++     +P EF
  S:    11 RIDKYIASNSSLSRADIQELIKSKAVFVNNGLVCKPSYIVHPPQEI--KIIRLLDKTPKIEAQNIKLDIIYEDDHLVIIDKPSGLIVHPSPTHYENTLANGLLYHFKNNLSDTNG-LLRPGIVHRIDKDTSGLLIVTKTNAVHIKLAEMFKNHSIKRSYIAICDNFLTDKKLRINLPIGLDPKNPQKRKVTNIKAKEAITNVELIKTFYHEKQPKSLVKCNLETGRTHQIRVHLAH-----INNPIYGDNVYNKKIDDFNQRLHAYKLEFFHPMLEKQMTFYSKVPSEF 291
>gi|167939375|ref|ZP_02526450.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus AH1134] (284 aa)
Score = 351, Expect = 2.2e-31, Identities = 94/250 (37%), Positives = 146/250 (58%)
  Q:     2 KNTQRLDILVSS-KFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK 251
           +  +R+D  V+      SR+  +  I++++VTVNGK + K N KV EE EI +   +   E   + P   ++EI YED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  +R GIVHR+DK T GL++VAK+  +  +     + + + ++Y A++H  +      +DAPI R +   R+ ++ D + K A T F+ + ++K+FTL E  L TGRTHQIRVH ++I   +  DP YGPK
  S:    13 QKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAV-KGNYKVKEEDEITVTIPE--PEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI--NG-VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIAR-DKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>gi|154496189|ref|ZP_02034885.1| hypothetical protein BACCAP_00473 [Bacteroides capillosus ATCC 29799] >gi|150274744|gb|EDN01808.1| hypothetical protein BACCAP_00473 [Bacteroides capillosus ATCC 29799] (304 aa)
Score = 350, Expect = 2.3e-31, Identities = 95/291 (32%), Positives = 148/291 (50%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  +S +   LSRS A+  +E   VT+ G  + K N K  E  E++L     VE   V  P    +++VYED  ++++NKP  ++VHP +     TL N + Y         NG+ LR GIVHR+D+ T GL+I AKS  +  A  +   D  + ++Y A+     +     V API R  T  ++     +  +EA T +  + ++   T  +  L TGRTHQIRVH   I + ++ D +YG K        GQ L A +L F+HP T + + +   +P  F+  + K
  S:    13 ERVDQFLSRQLPQLSRSAAQKLLEEGAVTLKGLPVKK-NYKTAEGDELVLSLPDPVEVDVV--PQDIPLDVVYEDGDVIVINKPVGMVVHPAAGHPDGTLVNALLYHCGKSLSGINGE-LRPGIVHRIDRDTSGLIIAAKSDFAHLALAEQLQDHSLYREYEAVAVGGFKEDEGTVRAPIARHPTDRKKMAVNFLQGREAVTHYTVLERFSGCTHLQCRLETGRTHQIRVHMAHIGHPLLGDTVYGSKKPYPGLA-GQCLHARRLSFVHPRTGERMTVECPLPDWFEAVLDK 299
>gi|169335052|ref|ZP_02862245.1| hypothetical protein ANASTE_01458 [Anaerofustis stercorihominis DSM 17244] >gi|169257790|gb|EDS71756.1| hypothetical protein ANASTE_01458 [Anaerofustis stercorihominis DSM 17244] (301 aa)
Score = 350, Expect = 2.4e-31, Identities = 103/294 (35%), Positives = 159/294 (54%)
  Q:     2 KNTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           K   R D  +S K    SR   K   +   V +N + + KP+ K+   E  ++ L E ++++      P    I IVYED+ ++IV+KP  ++VHP + + S TL N + Y    K +      +R GIVHR+DK T GL+I+AK+ ++ N     F +  I ++Y  + H  +   +  +DAPI R +   +       ++K A T F  I +Y  +T  +V L TGRTHQIRVH ++I + VI D +YG    I++  K GQ L AYKL FIHP T + +  N ++P  F E + +
  S:    12 KQNIRCDKFLSDKLEDFSRESLKKLFKEGEVFLNDEKV-KPSRKLIAGERVKVNLPEPEVLDVIAENIP----INIVYEDEDVVIVDKPQGMVVHPANGNHSGTLVNALMY--HVKDLSSINGVIRPGIVHRIDKDTSGLLIIAKNDNAHNHLAVQFKEHSINRRYKTICHGIIHENSGTIDAPIGRDKIKRKEMCVTQSNSKRAVTHFDVIKRYDKYTFLDVHLETGRTHQIRVHLKYISHPVIGDKVYGFNSQIDRPFK-GQLLHAYKLGFIHPKTNEYMEFNSELPDYFYELLDR 301
>gi|78044742|ref|YP_360337.1| ribosomal large subunit pseudouridine synthase A [Carboxydothermus hydrogenoformans Z-2901] >gi|77996857|gb|ABB15756.1| ribosomal large subunit pseudouridine synthase, RluA family [Carboxydothermus hydrogenoformans Z-2901] (305 aa)
Score = 350, Expect = 2.5e-31, Identities = 101/290 (34%), Positives = 164/290 (56%)
  Q:     6 RLDILVSSK--FSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY-KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  ++ +    LSRS  K  IE   VTVNG +  K + KV    EII        E  V  P +  ++IVYED+ +++VNK   ++VHP   +   TL N +  ++  + +   G  LR GIVHRLDK T GL++VAK+  +  +  +   ++K  ++Y  ++H +L+ +   +D PI R     R++++   + K A+T++K + ++ K FTL + +L TGRTHQIRVH  ++ + V+ DP YG ++ N      Q L A KL FIHP + + +     +P++F+  + K
  S:    17 RLDKFLAEQEELELSRSFIKKLIEEGKVTVNG-LHRKASYKV-RGGEIIAVLLPPPRELSV-KPEEIPLDIVYEDEDLVVVNKKAGMVVHPAEGNWDGTLVNAL--LYHCQNLSGIGGVLRPGIVHRLDKDTSGLLVVAKNDLAHQSLAEQIKEKKAVREYWTIVHGYLKNKEGIIDLPIGR-HPRDRQKMAVVSNGKTAQTVYKVLEEFNKGFTLIQAKLLTGRTHQIRVHFSYLGHPVLGDPKYGHQN-NPFGVKRQMLHAIKLSFIHPRSGELLEFTAPLPEDFQRVLAK 302
>gi|121593575|ref|YP_985471.1| ribosomal large subunit pseudouridine synthase D [Acidovorax sp. JS42] >gi|120605655|gb|ABM41395.1| ribosomal large subunit pseudouridine synthase D [Acidovorax sp. JS42] (334 aa)
Score = 349, Expect = 3.2e-31, Identities = 93/296 (31%), Positives = 160/296 (54%)
  Q:     2 KNTQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLAL-LHNHLQTRTVEVDAPIKRVETSTRREVSRDI---DAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIY-----GPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           ++ QRLD  ++      SRS  +  +    V +NG+ + KP ++V     I + E +  ++++   P +  +++VYED++IL+++KP  ++VHP   + S TL N +    D++ ++      R GIVHRLDK T GL++VA+S  + +A  ++   +++ ++Y+AL            V API R   +  R    D+     KEART F  I+  +   L    L TGRTHQIRVH   I++ ++ D +Y     GP H        Q L A++L F+HP T   +  +  +P++  + +  +G
  S:    36 QHAQRLDKALAELVPEFSRSYLQQLLLQGCVRLNGREVQKPASRVKVGDRIAV-EMRPTQQSQAFRPEQWPLDVVYEDEHILVIHKPAGLVVHPAPGNWSGTLLNAL-LGRDAQAMQVP----RAGIVHRLDKDTSGLMVVARSRSAMDALVRMIAAREVSRQYVALGWGGWTGAAHRSVHAPIGRDPRNRLRMAVVDLAQHPGKEARTDFDLIDANEEVCLVRCTLHTGRTHQIRVHMASIRHPLVADALYGGALAGPMH-------RQALHAFRLAFVHPVTGAALEFHAPLPEDMAQALDFWG 328
>gi|163812123|ref|ZP_02203802.1| pseudouridine synthase, RluA family [Dehalococcoides sp. VS] >gi|157404311|gb|EDO70352.1| pseudouridine synthase, RluA family [Dehalococcoides sp. VS] (300 aa)
Score = 349, Expect = 3.4e-31, Identities = 100/290 (34%), Positives = 160/290 (55%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +RLD  ++ K + LSRS  +  I++  V VNGK  +KP+ K+     I +  E   E    L      +EI+++DK +L++NKP  + VHP      +TL N +  +    K++   DPLR GIVHRLDK T GL++VAK+ ++    +  F ++ + K YL L+   L      ++AP+ R +   R++++   + + ART +K +   + ++L EV+L TGRTHQIRVH   I + V  D IYG K   +T    Q+L A++L F  P   + V     +P + +E +K
  S:    13 ERLDKYIAQKETDLSRSFIQALIDSGHVQVNGKT-AKPSLKLKNGDTITI--EISPETPPELKAEDIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLINGVLAL--EPKMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRETLANLSAQFKERTVRKYYLTLVKGELHPAEGFIEAPLGR-DPQNRQKIAVVSNGRHARTGYKVLRYIQGYSLLEVKLETGRTHQIRVHFAAIGHPVAGDAIYGQK---ETWLKRQFLHAHRLSFTLPSNGQTVEFTSPLPPDLEETLK 294
>gi|150390556|ref|YP_001320605.1| RluA family pseudouridine synthase [Alkaliphilus metalliredigens QYMF] >gi|149950418|gb|ABR48946.1| pseudouridine synthase, RluA family [Alkaliphilus metalliredigens QYMF] (310 aa)
Score = 349, Expect = 3.4e-31, Identities = 100/289 (34%), Positives = 161/289 (55%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKI-ISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLDI ++ ++  LSRS  +  I++N VTV+G+   ++   KV +   + L E K +E T    P    ++IVYED  +L+VNKP D++VHP   +  NT+ N + Y    K    NG  +R GIVHR+DK T GL++VAK+  +    ++   D    +KY  +    ++     ++API R +T  R +++     + A T  + +N++ + T  E +L TGRTHQIRVH  +I + ++ D +YG K  +K    GQ L A  L FIHP  +  +  N  +P  F++ ++
  S:    16 RLDIYIAEQYDDLSRSYIQKVIKDNGVTVDGRPEKNRYIVKVGQVIVVSLPEAKELEVTAQNIP----LDIVYEDDDLLVVNKPQDMVVHPAPGNYENTMVNALLYHCKGKLSSING-IIRPGIVHRIDKDTSGLLMVAKNNHAHQFLSEQLKDHSTTRKYHGISVGTIKEERATINAPIARHQTD-RLKMAVLAGGRNAVTHIQVLNRFGDHTYMEAQLETGRTHQIRVHLGYIGHPLLGDFVYGHKK-SKFNLKGQVLHAKTLGFIHPTKKTYMEFNAALPTYFEKLLR 299
>gi|168334458|ref|ZP_02692629.1| putative pseudouridylate synthase [Epulopiscium sp. 'N.t. morphotype B'] (304 aa)
Score = 349, Expect = 3.5e-31, Identities = 100/290 (34%), Positives = 165/290 (56%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHI-NKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           R+D  ++ +    +RS  + +IE  L+ +NGK+  ++   K  +  E  +   + V+    +TP +  ++I+YED  ILIVNKP +++VHP++   ++TL N + +         NG+ +R GIVHR+DK T GL++VAK+  S    + L  D  IE+KY AL++ +++     +D PI R     R++++   + + A T  + + ++ N T  E+ L TGRTHQIRVH   I + ++ DP+YG  KH+ N  T   Q L A  L FIHP +Q+ +     +P EF   I +
  S:    16 RVDKFLTEQLPQYTRSYIQKQIELGLLLINGKVAPARTRIKTGDTIEFTIAPPREVD----ITPSEIKLDIIYEDSDILIVNKPKNMVVHPSAGHYNDTLVNALLFYAKDSLSGINGE-IRPGIVHRIDKDTTGLLMVAKNDHSHVFLSDLLKDHNIERKYNALVYGNIKEDFFTIDRPIAR-NPKDRKKMAIVENGRRAVTECRVLERFGNATHIELSLQTGRTHQIRVHLTSIGHPLLGDPLYGRSKHLFNLQT---QMLHARVLGFIHPSSQQFMRFESVLPTEFLHTIGR 300
>gi|195978250|ref|YP_002123494.1| ribosomal large subunit pseudouridine synthase D [Streptococcus equi subsp. zooepidemicus str. MGCS10565] >gi|195974955|gb|ACG62481.1| ribosomal large subunit pseudouridine synthase D [Streptococcus equi subsp. zooepidemicus str. MGCS10565] (296 aa)
Score = 349, Expect = 3.8e-31, Identities = 94/291 (32%), Positives = 159/291 (54%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGK-IISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
            RLD  ++    LSRS A  +I+   V VNG    +K   +V +     + EE  ++      P    ++IVY+D  ++I+NKP  ++VHP++   + TL N +  ++  K +      +R GIVHR+DK T GL++VAK+  +          +K  +KY+A++H +L      ++API R +   R++ +     KEA T FK + ++  ++L E++L TGRTHQIRVH  +I + +  DP+YGP+        GQ+L A  L   HP T +E+   ++ P+ F+  +++
  S:    10 HRLDKALADLTPLSRSQANDQIKQKRVLVNGSPKKAKYIVQVGDCISYHIPEESSLDYQAQDIP----LDIVYQDDVLVIINKPQGMVVHPSAGHSTGTLVNAL--LYHVKDLSSINGVIRPGIVHRIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRGVIEAPIGRSDKD-RKKQTVTAKGKEALTRFKVLERFGRYSLVELQLETGRTHQIRVHMAYIGHPLAGDPLYGPR--KTLDGNGQFLHAQTLGLTHPVTGEELVFTVEPPEIFQRTLEQ 292
>gi|168182405|ref|ZP_02617069.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf] >gi|182674415|gb|EDT86376.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf] (305 aa)
Score = 349, Expect = 3.9e-31, Identities = 106/289 (36%), Positives = 159/289 (55%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKI-ENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ +S  F   SRS  +  I E N++  N K       KV +  E+ + E K++E    + P    ++I+YEDK +++VNKP +++VHP     S TL N +  +   K +       R GIVHR+DK T G+++VAK+  S N     F +  I + Y+AL+   ++     ++API R     R +++   D + A T +K I ++KN TL E  L TGRTHQIRVH   I + ++ DP+YG K      K GQ L A  L FIHP T++ V    ++P+ FK+ IK
  S:    16 RLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKKKKRNYKLKVGDNIEVNIPEPKLLE----IEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNAL--LNHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQGTIEAPIGR-HPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLK-GQMLHAKLLGFIHPTTRQYVEFESELPEYFKKIIK 298
>gi|85373063|ref|YP_457125.1| pseudouridine synthase D large subunit [Erythrobacter litoralis HTCC2594] >gi|84786146|gb|ABC62328.1| pseudouridine synthase D large subunit [Erythrobacter litoralis HTCC2594] (322 aa)
Score = 348, Expect = 4.2e-31, Identities = 93/293 (31%), Positives = 149/293 (50%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDA---KEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTK----YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  ++    LSR   K  ++   V V+G   + P+ K  E +   +     V+      P    +++V+ED+++L+VNKP  ++VHP + +   TL N + +    +    NG   R GIVHR+DK T GL++VAK+ ++       F +  I ++YLAL   H       ++  I R E   ++      D+   K A T +K + + ++  L E  L TGRTHQ+RVH + I + ++ DP YG  PK +    K      Q L A  L F HP T + V    D+P + +E I +  +
  S:    24 RLDKALAEASGLSRERVKALMQGGAVLVDGDPATNPSAKGSEGTPYTITLPPTVDPEA--QPQDIKLDVVFEDEHLLVVNKPAGMVVHPAAGNPDGTLVNALLHHCRGQLSGING-VARPGIVHRIDKDTSGLLVVAKTDNAHEGLAAQFAEHTINRRYLALCAGHPNPAEGTIEGRIGRSERDRKKMAPLPEDSSRGKHAVTHYKTLRRLRDCALIECRLETGRTHQVRVHCQSIGHPLLGDPTYGRDPKGLRPILKELGFARQALHAAMLGFEHPVTGQWVEFTADLPADMQELIDETAR 322
>gi|149187050|ref|ZP_01865357.1| pseudouridine synthase D large subunit [Erythrobacter sp. SD-21] >gi|148829339|gb|EDL47783.1| pseudouridine synthase D large subunit [Erythrobacter sp. SD-21] (318 aa)
Score = 348, Expect = 4.5e-31, Identities = 95/295 (32%), Positives = 152/295 (51%)
  Q:     1 MKNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESE--IILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDA---KEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTK----YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + +  RLD  ++    LSR   K  I + +V + GK     + KV E     I L   + +E      P    +++V+ED Y+L+VNKP  ++VHP + +   TL N + +    +    NG   R GIVHR+DK T GL++VAKS  +     K F D  I ++YLA    H    +  V   I R +   ++      D+   K A T ++ + +  +  L E  L TGRTHQ+RVH   I + ++ DP+YG  PK +  T +      Q L A +L FIHP + + ++   ++P +  E +++
  S:    11 LSSAGRLDKALADATGLSRERVKGLIADGVVEIAGKAARSASAKVAEGERYFIALPPPEPLETVAQDIP----LDVVFEDAYLLVVNKPAGMVVHPAAGNPDGTLVNALLHHCAGRLSGING-VARPGIVHRIDKDTSGLLVVAKSDAAHEGLAKQFADHSITRRYLAACAGHPNPPSGTVSGRIGRSDRDRKKMAVLPDDSTRGKHAVTHYETVRRLNHAALIECRLETGRTHQVRVHCASIGHALLGDPVYGRTPKPLRATLESLDFQRQALHAARLGFIHPISGESLDFCAELPPDMSELMRE 311
>gi|160945091|ref|ZP_02092317.1| hypothetical protein FAEPRAM212_02610 [Faecalibacterium prausnitzii M21/2] >gi|158442822|gb|EDP19827.1| hypothetical protein FAEPRAM212_02610 [Faecalibacterium prausnitzii M21/2] (310 aa)
Score = 348, Expect = 5.0e-31, Identities = 94/289 (32%), Positives = 155/289 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREV---SRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QR+D  +S + + LSRS  +  +    V  NGK ++K + K+     ++L+    + + K +    +DI  EIVYED ++L+VNKP  ++VHP   +   TL N + +          G+ +R GIVHR+DK T GL++VAK   +    ++      +E+ Y  +++         V+A + R +   ++     + +   K A T +K + +   FTL E  L TGRTHQIRVH   I + V  DP+YGP H   T+ +GQ L A  L F+HP T +++  + ++P  F  ++
  S:    15 QRIDRFLSGEDTGLSRSALQALVAEGHVQCNGKAVAK-SLKLKAGDTVLLE----IPDAKPIEAVPQDIPLEIVYEDAHLLVVNKPKGMVVHPAPGNPDGTLVNALLWHCKGSLSGIGGE-IRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYQTVVYGGFAQDEGFVEANLGRSKIDRKKMAVYPATEPHTKYAYTGYKVLERLGEFTLLECRLKTGRTHQIRVHMASIHHPVAGDPVYGP-HNCITSLHGQCLHAKTLGFVHPITGEQLRFDSELPDYFTHFL 302
>gi|116494944|ref|YP_806678.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei ATCC 334] >gi|116105094|gb|ABJ70236.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus casei ATCC 334] (306 aa)
Score = 347, Expect = 5.5e-31, Identities = 98/286 (34%), Positives = 159/286 (55%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVL--TPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           R+D ++ + + + +RS  +  +++ LVTVNG+  +K N KV     I +     + E K L   P    ++IVYED  +++V+KP  ++VHP       TL N + Y  D   I  NG  +R GIVHR+DK T GL++VAK+  +  + +     +   ++YLAL+H   +     +DAP+ R +   R+  +   D + A T F+ + +++++T  +  L TGRTHQIRVH  +I + V  DP+YGPK        GQ+L A KL F+HP T + +     +P  F++
  S:    13 RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAIS----IPEAKPLEAIPEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGI--NG-VIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGR-DPRDRKRQAVVADGRHAVTHFQVLERFEHYTFIKCILETGRTHQIRVHMAYIHHPVAGDPLYGPKR--TLPGKGQFLHAAKLGFVHPTTGQLLVFEAPVPPIFEK 290
>gi|91788477|ref|YP_549429.1| ribosomal large subunit pseudouridine synthase D [Polaromonas sp. JS666] >gi|91697702|gb|ABE44531.1| ribosomal large subunit pseudouridine synthase D [Polaromonas sp. JS666] (344 aa)
Score = 347, Expect = 5.8e-31, Identities = 90/281 (32%), Positives = 148/281 (52%)
  Q:    17 LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQ-TRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
            SRS  +  IE  +V +NG+ ++KP+ KV    E+I+ E +   +++   P    ++IV+ED Y+L+++KP  ++VHP   + S TL N +     ++  + +  P R GIVHRLDK T GL++VA+   + +    +   + + ++Y+AL H   Q  RT EV A I R   +  R  + D++    K A T+   +   +   L + +L TGRTHQIRVH   + + +I+D +YG        +  Q L A +L F HP T   +      P + +  I   G
  S:    61 FSRSYLQQLIEAAVVQLNGRAVTKPSAKVKAGDELII-ELRPTPQSQAFKPEAMALDIVFEDPYLLVIDKPAGLVVHPAPGNWSGTLLNGLL----ARDPQASFLP-RAGIVHRLDKDTSGLMVVARQRQAMDQLVSMIAARSVSREYIALAHGAWQGARTREVSAAIGRDPRNRLRMAAVDLEKNAGKPALTVISLLQNGERHCLVKCKLHTGRTHQIRVHMALLGHPLISDGLYGGAVAAGLER--QALHACRLAFEHPVTGAPMEFRSPPPPDLRAAIADVG 337
>gi|167771408|ref|ZP_02443461.1| hypothetical protein ANACOL_02774 [Anaerotruncus colihominis DSM 17241] >gi|167666048|gb|EDS10178.1| hypothetical protein ANACOL_02774 [Anaerotruncus colihominis DSM 17241] (306 aa)
Score = 346, Expect = 7.5e-31, Identities = 82/229 (35%), Positives = 124/229 (54%)
  Q:    65 LTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           + P    IEIVYED  +L+VNKP  ++VHP     + TL N + Y    +    NG  +R GIVHR+DK T GL+IVAK+  +     +   +    + Y A+++    T    VDAPI R +   ++    D +A+ A T ++ + +   FT  ++ L TGRTHQIRVH  +I + V  DPIYGP+    T+ +GQ L A  + F HP T   +  + ++P  F  ++
  S:    74 IVPQDIPIEIVYEDGDLLVVNKPKGMVVHPAPGHPNGTLVNALLYHCQGRLSSING-VIRPGIVHRIDKDTSGLLIVAKNDAAHGTLAEQIKNHSFTRIYNAVVYGGFSTDEGTVDAPIGRSQNDRKKMCVTDRNARGAVTHYRVLERLGRFTWLKLCLETGRTHQIRVHMAYIGHPVAGDPIYGPQK-TITSLHGQCLHARVIGFHHPRTGVYMEFSSELPDYFSTFL 300
>gi|62184670|ref|YP_219455.1| putative pseudouridine synthase [Chlamydophila abortus S26/3] >gi|62147737|emb|CAH63481.1| putative pseudouridine synthase [Chlamydophila abortus S26/3] (325 aa)
Score = 346, Expect = 7.8e-31, Identities = 103/293 (35%), Positives = 162/293 (55%)
  Q:     3 NTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTK-VDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           N  RLD  LVS     SR+  +  I +  VT+N +I +K +T+ V  ++  I  EEK  EE   L P    +E +YED+ IL++NKP D++VHP       T+ + ++  I +  K ++  +P R GI+HRLDK T GL+I AK+  +   +++LF  ++++K YLA+         +     + R  T  R+E++     KEA T  + +     F+L  +   TGRTHQ+RVH + +   ++ DP+YG    N    YG   Q L AY + FIHP T K +N+  ++P++ K  I K
  S:    15 NRDRLDKFLVSQNPKYSRAFYQQHIVDQRVTINEQIQTKVSTQLVPGDTVSITIEEK--EEPSELLPEAIPLEKIYEDEMILVINKPRDMVVHPAPGHTRGTVVHALLHEIGERLKQEFPEEPWRPGIIHRLDKDTSGLLITAKTRQAKMIYSELFATKQLKKSYLAICVGKPSASVIHTK--LARHHTK-RKEMAVSSTGKEAITRCEVLAYNGKFSLVLLHPETGRTHQLRVHMKHLSTPILGDPVYGSASANSC--YGLDKQQLHAYSVNFIHPQTHKHLNLTTELPRDMKILIIK 306
>gi|81428560|ref|YP_395560.1| pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei subsp. sakei 23K] >gi|78610202|emb|CAI55251.1| Pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei subsp. sakei 23K] (301 aa)
Score = 345, Expect = 1.1e-30, Identities = 97/292 (33%), Positives = 162/292 (55%)
  Q:     4 TQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           T R+D ++S      SRS  +  ++ +LV +NG+  SK N KV  DE+  + + +   ++    L P    ++IVYED  +L+VNKP  ++VHP+    + TL N +  +  +   + NG   R GIVHR+DK T GL++VAK+ ++  + ++    +   ++YLAL+H +++     +DAPI R +    ++     D + A T F+ + ++ ++TL    L TGRTHQIRVH  +I   V  DP YGP+        GQ+L A  L F HP T + +     +P  F++ +++
  S:    13 TGRIDKVLSQLLPDYSRSQIQQWLKKDLVEINGQT-SKGNHKVVADEKISVTIPDPVSLD----LVPEDIPLDIVYEDDQVLVVNKPQGMVVHPSPGHPNGTLVNAL--LAHTPLSEING-VFRPGIVHRIDKDTSGLLMVAKTNEAHESLSEQLKAKSNLREYLALVHGNIEEDEGTIDAPIGRSKLDRMKQAIVP-DGRPAVTHFEVVERFTDYTLIRCRLETGRTHQIRVHLAYINRPVAGDPTYGPR--KTLPGKGQFLHAAVLGFKHPTTGENMRFEAPLPAIFEKTLQE 296
>gi|170288274|ref|YP_001738512.1| RluA family pseudouridine synthase [Thermotoga sp. RQ2] >gi|170175777|gb|ACB08829.1| pseudouridine synthase, RluA family [Thermotoga sp. RQ2] (311 aa)
Score = 344, Expect = 1.2e-30, Identities = 101/290 (34%), Positives = 167/290 (57%)
  Q:     6 RLDILVSSKFS--LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNF-TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  +  K    +SRS+ +  I+   V VNG+I  KP+ K+ +E EI+  +     +   + P + +++++YED+ I++++KP D+IVHP    LS TL N +  +   K ++  G  LR GIVHRLDK T G+++VAK+  +  + +K F D+K++K Y+ L+   +++    +D P+ R     R +++     KEA T ++ + ++ +  TL      TGRTHQIRVH + + + ++ D IYG PK         Q L A KL F HP T K +     +P++FKE I++
  S:    14 RLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQI-KKPSYKL-KEGEIVEVDLPEKPQEATVQPEEIELKVLYEDRDIVVIDKPGDMIVHPVPSKLSGTLVNAL--LHHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYILLVKGRVKSDEGVIDLPLAR-HPVLRIKMAVVETGKEAITEYRVLKRFDDVATLVLAFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEIFGIKRQMLHALKLGFFHPRTGKWMEFVSPLPEDFKEAIRR 302
>gi|124516586|gb|EAY58094.1| Pseudouridylate synthase, 23S RNA-specific [Leptospirillum sp. Group II UBA] (339 aa)
Score = 344, Expect = 1.2e-30, Identities = 94/291 (32%), Positives = 159/291 (54%)
  Q:     5 QRLDILVSSK-FSLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSK----------KIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY-KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +RLDI +S      +RS  +  +E  LVT+N  I    + KV   +   +++   +    ++   P    +EI+YED+ +++++KP  ++VHP     S TL N + + F S+          + +    PLR G+VHRLD+ T G+++V K+          F D+ + KKYLAL+   L  +  E++API R  T  R++ +   D K + T ++ +  Y +N++L EV L TGRTHQIRVH  ++   ++ D +YG K         Q L A+KL F HP +  ++     +P +F   +++
  S:    30 KRLDIYLSKNCLGFTRSRVQRLLEEKLVTIN-DIYPASSHKVRGGDRIRVLIPPPR----SQTAQPENIRLEILYEDEDLIVISKPPGLVVHPAPGHSSGTLVNGLLFHFQSQGDEQKKGEPEEEEEAERPLRAGLVHRLDQDTSGVMVVGKTESVVLDLMNQFKDRSVSKKYLALVKGILPKKRGEINAPIGR-STHDRKKFTVRQDGKPSVTRYRVLETYHENYSLLEVTLLTGRTHQIRVHFRYLGFPLLGDAVYGSKGTENKNFPRQMLHAWKLSFQHPSSNSKMEFEAPLPPDFVSALER 328
>gi|118443119|ref|YP_878025.1| ribosomal large subunit pseudouridine synthase D [Clostridium novyi NT] >gi|118133575|gb|ABK60619.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Clostridium novyi NT] (304 aa)
Score = 344, Expect = 1.2e-30, Identities = 104/293 (35%), Positives = 167/293 (56%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD+ +S  F   SRS A+  IE+  V VNG I  S    K  +  E+ +KE+    ET  + P    + I+YED+ +++++KP  ++VHP + + S TL N + Y  DS     NGD +R GIVHR+DK T G+++VAK+ ++    ++   +  ++++Y+AL+   ++     +D P+ R  +   +R V R+   K A T ++ I ++   TL +  L TGRTHQIRVH   I + ++ DP+YG K   +    GQ L A KL FIHP ++K +    ++P  +KE + K  K
  S:    16 RLDVFISKCFEEKSRSYAQKLIEDKNVLVNGSIKKSNYKLKTGDNVEVTIKED----ETINIEPEDIKLNILYEDEDVIVIDKPQGMVVHPGNGNYSGTLVNGLLYHCDSLS-SINGD-VRPGIVHRIDKDTSGVLVVAKNDNAHIILSEQLKEHSMKREYVALVEGIIKDDEGTIDEPLGRNPKDRIKRAVVRN--GKNAITHYEVIRRFNKNTLVKCILETGRTHQIRVHMAHINHPLVGDPMYGFKK-QRFKLNGQMLHARKLGFIHPSSKKYMEFQSELPNYYKEILFKLSK 302
>gi|56807621|ref|ZP_00365521.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus pyogenes M49 591] (218 aa)
Score = 344, Expect = 1.2e-30, Identities = 84/218 (38%), Positives = 130/218 (59%)
  Q:    77 EDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           ED  + I+NKP  ++VHP+    S T+ N + Y I D   I  NG  +R GIVHR+DK T GL++VAK+  +  A  +    +K  +KYLA++H +L      ++API R E   R++ +     KEA T F  + ++ +++L E++L TGRTHQIRVH  +I + V  DP+YGP+     + +GQ+L A  L   HP T KE+   ++ P+ F++ +K
  S:     1 EDDTLAIINKPQGMVVHPSVGHPSGTMVNALMYHIKDLSSI--NG-VVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKD-RKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR--KTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLK 213
>gi|182417977|ref|ZP_02949285.1| ribosomal large subunit pseudouridine synthase D [Clostridium butyricum 5521] >gi|182378148|gb|EDT75683.1| ribosomal large subunit pseudouridine synthase D [Clostridium butyricum 5521] (304 aa)
Score = 344, Expect = 1.2e-30, Identities = 99/290 (34%), Positives = 162/290 (55%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           R+D  +S+ F   SRS  +  IE   V VN K + K N K+ +  EI    E ++ E ++L+   ++I  +IVYED+ +++VNK   ++VHP   + + TL N +  ++  K +      +R GIVHR+DK T G++++AK+ D+ N  ++   D  ++++Y AL+   L+     +D P+ R +   R ++    D K A T ++ + +Y  +TL +  L TGRTHQIRVH   I   ++ DP+YG K   K    GQ L A  L FIHP T + +    ++P+ F + I K
  S:    16 RIDKYLSNIFKDKSRSFIQGLIEKENVKVNSKTL-KSNYKLKKADEI----EIMIPEPEILSVEAENIPIDIVYEDEDVIVVNKAQGMVVHPAPGNYNGTLVNAL--LYHCKDLSSINGVIRPGIVHRIDKDTSGILVIAKNDDAHNKLSEQLKDHSMKREYYALIEGRLKNNDGTIDKPLGRCKKD-RLKIGIIEDGKRAVTHYEVVERYNGYTLVKCVLETGRTHQIRVHMASIGFPLVGDPLYGFKR-QKFKLEGQVLHARTLGFIHPRTGEYMEFTSELPQYFCDLINK 299
>gi|46445989|ref|YP_007354.1| 23S RNA-specific pseudouridine synthase D [Candidatus Protochlamydia amoebophila UWE25] >gi|46399630|emb|CAF23079.1| probable 23S RNA-specific pseudouridine synthase D [Candidatus Protochlamydia amoebophila UWE25] (318 aa)
Score = 344, Expect = 1.3e-30, Identities = 94/291 (32%), Positives = 157/291 (53%)
  Q:     5 QRLDILVSSKFS--LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +RLD +++ +F+   SR+  +  I+ +L+ VNG I  K  T + E  E+  + + +      L P    + I+YED+++L++NKP  ++VHP   + S T  N + Y    +K+    D +R GIVHRLDK T GL++ AK+L++     +LF  +K+ K YLA+     +    E+ API R     R++++     K A +  K +      +  ++E+ TGRTHQIRVH ++  + ++ DP+YG   +N+      Q L A  L+F HP + + +      P E    IKK
  S:    21 ERLDKVLARRFNAKYSRTYFQFLIDKHLILVNG-IAVKKRTLLQEGDEV--EVQFLASPESNLMPENIPLSILYEDEHLLVINKPAGMVVHPAPGNWSGTFVNALLYY--CQKLPLLPDTIRPGIVHRLDKGTSGLLVAAKTLETQQKLIELFASRKVYKAYLAICIG--RPADGEIQAPIGR-HPIHRKQMAVIPTGKPAISFCKTLGWSDKLSFVQIEIATGRTHQIRVHMKYRGSPILGDPLYGQISLNQYYSVPHQLLHAAVLRFQHPISLENLEFCTPPPPEMVRLIKK 306
>gi|170756442|ref|YP_001781114.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str. Okra] >gi|169121654|gb|ACA45490.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str. Okra] (305 aa)
Score = 344, Expect = 1.4e-30, Identities = 104/289 (35%), Positives = 158/289 (54%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTK-VDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ +S  F   SRS  +  I+   V VN K   +     V +  E+ + E K+++    + P    ++I+YEDK +++VNKP +++VHP     S TL N +  +   K +       R GIVHR+DK T G+++VAK+  S N     F +  I + Y+AL+   ++     ++API R     R +++   D + A T +K I ++KN TL E  L TGRTHQIRVH   I + ++ DP+YG K      K GQ L A  L FIHP T++ V    ++P+ FK+ IK
  S:    16 RLDLYLSKIFEDKSRSYLQGIIDQGSVLVNNKKKKRNYKLKVGDNIEVNIPEPKLLQ----IEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNAL--LHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQGTIEAPIGR-HPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLK-GQMLHAKLLGFIHPTTEQYVEFESELPEYFKKIIK 298
>gi|169831112|ref|YP_001717094.1| RluA family pseudouridine synthase [Candidatus Desulforudis audaxviator MP104C] >gi|169637956|gb|ACA59462.1| pseudouridine synthase, RluA family [Candidatus Desulforudis audaxviator MP104C] (309 aa)
Score = 344, Expect = 1.4e-30, Identities = 98/290 (33%), Positives = 153/290 (52%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD+ ++ +   LSR+  +  I   LVTVNG+  ++ + +V     + LK      ET  + P    +E+ +ED  +L+VNKP  ++VHP     S TL N ++ +  D   I  NG  LR GIVHRLD+ T GL++VAK+  +  A      D+ + ++Y AL+H   +  T  VDAPI R     +R        + ART ++ + ++  F+L E+ L TGRTHQIRVH   + + ++ D  YG        + GQ+L A  L F HP T + +     +P E    +++
  S:    17 RLDVFLAGQNPELSRARIQKLISLELVTVNGRP-ARASHRVRGGDCVELKVPD--PETPRIEPEAIPLEVCFEDPDVLVVNKPRGLVVHPAVGHYSGTLVNALLHHCRDLSGI--NG-ILRPGIVHRLDRDTSGLLMVAKNDAAHLALAGQLKDRAVLRRYTALVHGRPRRETGTVDAPIGRHPRDRQRMAVTPRSGRAARTHYRVVRRFDKFSLLELTLDTGRTHQIRVHMAHVGHPLVGDLKYGHARPELGLE-GQFLHAGTLGFRHPRTGEVLVFEAPLPSELAAVLER 301
>gi|196191145|gb|EDX86109.1| pseudouridine synthase, RluA family [Synechococcus sp. PCC 7335] (309 aa)
Score = 343, Expect = 1.5e-30, Identities = 90/286 (31%), Positives = 150/286 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVS---RDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +RLD  ++    + SR+  +  IE   V+VNG++  +    V     IIL   +   +   LTP    ++I+YED  +LIVNKP  ++VHP     + TL + + + +  +++   G   R GIVHRLDK T G ++VAK+  +     +    +  +++YL +++   +     +D PI R     R+++S    +   + A T +K + +  N+TL   +L TGRTHQIRVH+ ++   +I DP YG          GQ L A++L   HP TQ  V+    +P ++K
  S:    13 ERLDRWLADNVEAFSRNRVQQLIEQGAVSVNGEVCDRKKELVTAGDYIILSVPE--AQPYELTPEDIPLDILYEDDQLLIVNKPAGMVVHPAPGHATGTLVHALLF-YCGEQLTGVGGVQRPGIVHRLDKNTTGAMVVAKTETALCNLQQQIQAKTAKREYLGIVNGAPKAEQGTIDQPIGR-HPKHRKKMSILPVESGGRTAITHWKTVERLGNYTLIHFQLETGRTHQIRVHSAYLGLPIIGDPDYGSTRFPGVKLPGQALHAFRLTLSHPITQAVVSAEAPLPDQWK 298
>gi|91200050|emb|CAJ73092.1| similar to ribosomal large subunit pseudouridine synthase D [Candidatus Kuenenia stuttgartiensis] (335 aa)
Score = 343, Expect = 1.6e-30, Identities = 87/285 (30%), Positives = 161/285 (56%)
  Q:     4 TQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHI---------NKTTKYG-----QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           ++R+D  +SS+F  LSR+  +  ++   + VNG ++   ++   ++ ++I     + EETK+ TP    + I+YED Y++++NKP D++VHP     S TL N +   F  + +     PL+ GIVHRLD+ T G+++V KS    +     F  + ++K+Y A++   +   + E++ PI R     ++   R    K A ++++ I +++ +TL ++   TGRTHQIRVH + I + V+ D +Y   +           +    G     Q L A++++F HP   K++   +DM ++
  S:    25 SKRIDRFISSRFPDLSRTYIQKLVKEGAIVVNGNVVK--SSYFIKKGDVISATVPVPEETKI-TPEDIPLNIIYEDDYLMLINKPYDMVVHPAGGHPSGTLVNAVT--FYCQNLSQINGPLKAGIVHRLDRDTSGVMLVIKSDAVHSHIAMQFEKRLVKKEYFAVVEGEVAFDSNEINMPIGRHRVDRQKMAVRRDTGKNATSVYEVIERFRGYTLVKIMPKTGRTHQIRVHMQAIGHPVVADEMYSKYNACFRSDLLGKERAPDEGSIIERQALHAHRIEFFHPILNKQMAFQVDMAED 319
>gi|1143378|dbj|BAA09443.1| ORFX [Zymomonas mobilis] (317 aa)
Score = 343, Expect = 1.6e-30, Identities = 82/228 (35%), Positives = 127/228 (55%)
  Q:    67 PWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRR-EVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKH------INKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           P    +EIV+ED+++L+VNKP  ++VHP + +  NTL N + Y   + K+   G   R GIVHR+DK T GL++VAK+  +       F D  I ++Y A++  +   +   VDAP+ R   + ++  +  D   K A T +  I   KN +L E  L TGRTHQ+RVH   I + ++ DP+YG         +       Q L A  L FIHP + K+V+ + +MP++ +   K
  S:    77 PQDIPLEIVFEDEHLLVVNKPAGMVVHPAAGNYDNTLVNALLY-HCAGKLSGIGGVARPGIVHRIDKDTSGLLVVAKTDPAHAGLAAQFADHSINRRYRAIVDGNPSLQG-HVDAPLARSSVNRQKMAIVSDGRGKRAVTHYCMITPLKNASLIECRLETGRTHQVRVHMSSIGHSLLGDPVYGRSKKAHHALLQSLAFQRQALHAAHLGFIHPISGKQVDFDAEMPQDMQLLFK 309
>gi|187779872|ref|ZP_02996345.1| hypothetical protein CLOSPO_03468 [Clostridium sporogenes ATCC 15579] >gi|187773497|gb|EDU37299.1| hypothetical protein CLOSPO_03468 [Clostridium sporogenes ATCC 15579] (305 aa)
Score = 343, Expect = 1.7e-30, Identities = 104/289 (35%), Positives = 158/289 (54%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKP-NTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ +S  F   SRS  +  I+   V VN K   +    KV +  ++ + E K+++    + P    ++I+YEDK +++VNKP +++VHP     S TL N +  +   K +       R GIVHR+DK T G+++VAK+  S N     F +  I + Y+AL+   ++     ++API R     R +++   D + A T +K I ++KN TL E +L TGRTHQIRVH   I + ++ DP+YG K      K GQ L A  L FIHP T + V     +P+ FK+ IK
  S:    16 RLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIKVNIPEPKLLQ----IEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNAL--LSHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDGQGTIEAPIGR-HPVDRIKMAVVKDGRYAVTHYKVIERFKNHTLVECKLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLK-GQMLHAKLLGFIHPTTGQYVEFESQLPEYFKKIIK 298
>gi|27262446|gb|AAN87504.1| Ribosomal large subunit pseudouridine synthase D [Heliobacillus mobilis] (327 aa)
Score = 343, Expect = 1.7e-30, Identities = 98/289 (33%), Positives = 160/289 (55%)
  Q:     6 RLDI-LVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEI-ILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY--KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ LV+ +   SR+  ++ I+  L+ V G  + K N ++     I ++  E +  E   + P    I+IVY+D ++ ++NK   ++VHP     S TL N + Y I D   I  NG+ LR GIVHR+DK T GL++VAK  ++     +   D  + ++YLA++H  +   T  +DAPI R +   R++++     K + T  + + ++    F+L    L TGRTHQIRVH  +I + V  DP YGPK      + GQ L A++L F HP   +E+    + P+ F++ ++
  S:    37 RLDVWLVNRELVPSRTHGQNWIKEGLIKVEGMTV-KANYRLRPGDRIEVVPAEPVSTE---IIPENIPIDIVYQDAHVAVINKSAGLVVHPAEGHTSGTLVNALLYHIKDLSGI--NGE-LRPGIVHRIDKDTSGLLVVAKHDEAHIHLAEQVKDHLVRREYLAIVHGIIGAETGRIDAPIGR-DPKDRQKMAVVSSGKASVTHLRVLERFPESGFSLVRCNLETGRTHQIRVHMAYIGHPVAGDPKYGPKKAAFGLE-GQALHAHRLDFTHPHDGREMTFQAEPPETFQKVLE 321
>gi|120610104|ref|YP_969782.1| ribosomal large subunit pseudouridine synthase D [Acidovorax avenae subsp. citrulli AAC00-1] >gi|120588568|gb|ABM32008.1| ribosomal large subunit pseudouridine synthase D [Acidovorax avenae subsp. citrulli AAC00-1] (339 aa)
Score = 342, Expect = 2.0e-30, Identities = 88/281 (31%), Positives = 151/281 (53%)
  Q:    17 LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQ-TRTVEVDAPIKRVETSTRREVSRDI---DAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
            SRS  +  +    V VNG+  +KP+ +V +  +++  E +   +++   P    ++ VYED+++ IVNKP  ++VHP   + S TL N +    D +     G+  R GIVHRLDK T GL++VA+     +A  ++   +++ ++YLAL H   Q  +T  V+  I R   +  R  + D+     K ART    ++  +N  L    L TGRTHQIRVH  ++++ ++ D +YG +     ++  Q L AY+L F HP T + +  +  +P +    ++ +G
  S:    57 FSRSYLQQLLGEGGVLVNGRAAAKPSARV-QAGDVLSVELRPTPQSQAFRPEAMALDTVYEDEHLRIVNKPAGLVVHPAPGNWSGTLLNGL-LALDPRA----GNVPRAGIVHRLDKDTSGLMVVARERSVMDALVRMIAAREVSRQYLALGHRAWQGAQTRVVEEAIGRDPRNRLRMAAVDLAVHAGKPARTDIAVLDTCENGCLVHCTLHTGRTHQIRVHMAWLRHPLVADALYGGEPAAGLSR--QALHAYRLAFAHPVTGQPLLFHAPLPGDMAGALQAWG 333
>gi|89211512|ref|ZP_01189874.1| Pseudouridine synthase, RluD [Halothermothrix orenii H 168] >gi|89158889|gb|EAR78575.1| Pseudouridine synthase, RluD [Halothermothrix orenii H 168] (308 aa)
Score = 342, Expect = 2.0e-30, Identities = 102/275 (37%), Positives = 150/275 (54%)
  Q:    17 LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           LSRS  +  I+N+ V VNG+ + K + KV+    I L       E   + P + D++I+YEDK IL++NK   ++VHP   +  NTL N +I Y  +   I     P   GIVHRLDK T G++++AK+  S     + F  +K +K Y  LL   L  +  ++DAPI R     ++      ++K+A T FK +  +++ +  EVEL TGRTHQIRVH  ++   V+ D IYG K  N+     Q L AY+L F HP   K V     +P +FK+
  S:    30 LSRSYIQKLIDNDKVLVNGESV-KRSFKVNRGDHIRLIIPP--PEDSGIKPVEMDLDIIYEDKDILVLNKNAGLVVHPAPGNHENTLVNALIAYCDNLSTISGVNRP---GIVHRLDKDTSGVMVIAKNDISHRKLVEQFKQRKTKKYYRTLLKGELPYKEGKIDAPIGRDPHDRKKMAVTRKNSKKAVTYFKVLEFFRDHSYVEVELKTGRTHQIRVHFSYMGFPVVGDSIYGKKR-NRLQATRQLLHAYRLGFYHPRNDKWVEYKASLPDDFKK 298
>gi|160947739|ref|ZP_02094906.1| hypothetical protein PEPMIC_01674 [Peptostreptococcus micros ATCC 33270] >gi|158446873|gb|EDP23868.1| hypothetical protein PEPMIC_01674 [Peptostreptococcus micros ATCC 33270] (310 aa)
Score = 342, Expect = 2.1e-30, Identities = 104/284 (36%), Positives = 155/284 (54%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           R D+ +S K S LSR+  +  I+  LV VNGK I KPN  ++   EI +      E T  L     D++IVYED YI+I+NKP +++VHP   +  +TL N +  +   K    N +  R GIVHRLDK T GL+I AK  ++     ++F +++I KKYLA+ +         +D PI R E   ++   +    K A T +  +     ++L +V L TGRTHQIRVH   + + +I D  YG K+  K    GQ L +Y L+F HP T + ++  + +P E+
  S:    13 RCDVFLSEKISNLSRTSIQKLIKGKLVFVNGKNI-KPNVILEIGDEITVSIPDKKEIT--LVAEDIDLDIVYEDDYIIIINKPRNMVVHPAVGNEKHTLVNAL--LNHCKLSMINSE--RPGIVHRLDKDTTGLIICAKDDETHLKLVEMFANREINKKYLAICNGSFSKENGLIDKPIGRDEKDRKKMSVKSKSGKAAITEYNVLISNLKYSLVDVTLHTGRTHQIRVHFSSLNHPIIGDETYGKKN-EKIKANGQMLHSYYLEFSHPITDENLSFTV-LPDEY 288
>gi|57233860|ref|YP_182086.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides ethenogenes 195] >gi|57224308|gb|AAW39365.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Dehalococcoides ethenogenes 195] (300 aa)
Score = 342, Expect = 2.5e-30, Identities = 97/290 (33%), Positives = 160/290 (55%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +RLD  ++ K + LSRS  +  +E   + VNGK  +KP+ K+     I +  E   E    L      +EI+++DK +L++NKP  + VHP      +TL N +  +    +++   DPLR GIVHRLDK T GL++VAK+ ++    +  F ++ + K YL L+   L      ++AP+ R +   R++++   + + ART +K +   + ++L EV+L TGRTHQIRVH   I + V  D +YG K   +T    Q+L A++L F  P   + V  +  +P + +E +K
  S:    13 ERLDKYITQKETDLSRSFIQELVEAGHIQVNGKN-AKPSLKLKNGDTITI--EIPPETPPELKAEDIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLINGVLAL--EPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNREALANLSAQFKERTVRKYYLTLVQGELHPAEGFIEAPLGR-DPQNRQKIAVVSNGRPARTGYKVLRYIQGYSLLEVKLETGRTHQIRVHFAAIGHPVAGDAVYGQK---ETWLKRQFLHAHRLSFSLPSNGQNVEFSSPLPPDLEEALK 294
>gi|152981261|ref|YP_001353083.1| ribosomal large subunit pseudouridine synthase D [Janthinobacterium sp. Marseille] >gi|151281338|gb|ABR89748.1| ribosomal large subunit pseudouridine synthase D [Janthinobacterium sp. Marseille] (342 aa)
Score = 341, Expect = 3.0e-30, Identities = 98/292 (33%), Positives = 158/292 (54%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINK----YKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           RLD ++S+     SRS  +  I+   V+V+G++     T   +E  +I  +     E +   P   D+ IV+ED  +L++NKP  ++VHP + + S TL N + +   S     +G P R GIVHRLDK T GL++VAK+L +     +    + ++++YLAL+       T ++DA I R      +  VS ++ AK A T F+ +       +  +L    L TGRTHQIRVH + I   ++ D +YG +H+  T    Q L A +L  IHP + + V  + ++P++F E I + G
  S:    50 RLDKVLSTLVPQYSRSRLQQWIDGGHVSVDGEVARAKMTVYGDEKVVIYPQP--APEDEAFKPEAMDLAIVHEDAEMLVINKPAGLVVHPAAGNWSGTLLNGLLHYLPS----ISGVP-RAGIVHRLDKDTSGLMVVAKTLIAHTDLVRQLQARTVKREYLALVWGTPNI-TGKIDASIGRHARDRIKMAVSENLTAKPAVTHFQRLATGMLDGRPVSLMLCRLETGRTHQIRVHMQSIGFALVGDGLYGKQHLT-TVFPRQALHARRLGLIHPVSGEAVEWSSELPQDFAELIARAG 338
>gi|161507611|ref|YP_001577565.1| pseudouridine synthase [Lactobacillus helveticus DPC 4571] >gi|160348600|gb|ABX27274.1| pseudouridine synthase [Lactobacillus helveticus DPC 4571] (303 aa)
Score = 341, Expect = 3.1e-30, Identities = 97/293 (33%), Positives = 161/293 (54%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVL--TPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD  +S +   LSR+  K  ++   + VN K+  K + K+    +I    E  V   K L   P    ++IVYED+ +++VNKP  ++VHP      +TL N +  ++ ++ +  + +  R GIVHR+DK T GL+++AK+  +  +       +  ++ Y A++H         +DAPI R     R++++   + K+A T FK + ++K ++L E +L TGRTHQIRVH ++I + V  DP+YGP+   K    GQ+L A  L F HP T K +    + PK F++ + +  K
  S:    15 RLDKFISEQIPDLSRTRVKELVKEKEILVNHKV-EKVSYKIQAGDKI----EINVPAVKPLDVVPENIPLDIVYEDEVVIVVNKPQGMVVHPAPGHPDHTLVNAL--LYHTQDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKRIYWAIVHGDFGEENGVIDAPIGR-NPYDRKKMAVVENGKKAVTHFKVLKQFKGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGN--GQFLHAKVLGFKHPRTGKWLEFTAEPPKIFQDTLAQLEK 300
>gi|186455348|ref|ZP_02965662.1| pseudouridine synthase, RluA family [bacterium Ellin514] >gi|184207426|gb|EDU04471.1| pseudouridine synthase, RluA family [bacterium Ellin514] (318 aa)
Score = 340, Expect = 3.4e-30, Identities = 94/287 (32%), Positives = 153/287 (53%)
  Q:     4 TQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKP--NTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP---KHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           ++RLD  +  +F ++SR   +  IE   + VNG+ I KP  + +  E  E+   E +  E      P    ++I++ED  +L++NK   ++VHP +    +TL N + +  + + +   G   R GIVHRLDK T G ++VAK+  +  A  + F  + +EK YLA++   +   + E+ A I R  T  +R    D   +EA T +K   ++   T  E  L TGRTHQIRVH + +   ++ D  YG    K + + T Y    Q L A+KL F+HP   K+++     P +F+
  S:    17 SERLDTFLRERFPAVSRGTIQRLIEQGHIKVNGQTI-KPTHHPRAGELIEVYWPEARPAEAR----PEDIPLDIIFEDSDLLVLNKAPGLVVHPAAGHEEHTLVNALLHHCEGQ-LSGIGGVARPGIVHRLDKETSGCLVVAKNDAAHMALAEQFSGRTLEKTYLAIVCGEVVRNSGEIRASIARHPTHRKRMTVTDGSGREAWTSYKVRERFSGATWLEALLHTGRTHQIRVHFQHLGYPIVGDATYGTRQNKRLIEVTGYAAPRQMLHAWKLSFLHPCKGKKLSFEAPWPADFQ 306
>gi|191638454|ref|YP_001987620.1| Pseudouridine synthase [Lactobacillus casei] >gi|190712756|emb|CAQ66762.1| Pseudouridine synthase [Lactobacillus casei BL23] (307 aa)
Score = 340, Expect = 3.5e-30, Identities = 97/286 (33%), Positives = 158/286 (55%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVL--TPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           R+D ++ + + + +RS  +  +++ LVTVNG+  +K N KV     I +     + E K L   P    ++IVYED  +++V+KP  ++VHP       TL N + Y  D   I  NG  +R GIVHR+DK T GL++VAK+  +  + +     +   ++YLAL+H   +     +DAP+ R +   R+  +     + A T F+ + +++++T  +  L TGRTHQIRVH  +I + V  DP+YGPK        GQ+L A KL F+HP T + +     +P  F++
  S:    14 RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAIS----IPEAKPLEAIPEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGI--NG-VIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGR-DPRDRKRQAVVAAGRHAVTHFQVLERFEHYTFIKCILETGRTHQIRVHMAYIHHPVAGDPLYGPKR--TLPGKGQFLHAAKLGFVHPTTGQLLVFEAPVPPIFEK 291
>gi|116629656|ref|YP_814828.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri ATCC 33323] >gi|116095238|gb|ABJ60390.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus gasseri ATCC 33323] (304 aa)
Score = 340, Expect = 3.6e-30, Identities = 94/289 (32%), Positives = 168/289 (58%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD +++ K   LSR+  K  + +  + VN K   K + KV     I    +  V   K L+   +++  +IVYED  +++VNKP  ++VHP++    +TL N +  ++ + ++  + +  R GIVHR+DK T GL++VAK+  +  +  K   ++  +++YLA++H + +T+   +DAPI R   + R++++ +   K A T F  + ++K+++L +  L TGRTHQIRVH ++I + +  DP+YGPK       +GQ+L A  L F  P T K +  +  +P  F++ ++
  S:    15 RLDKVIAEKLKDLSRTKIKELVNDKNILVNHKA-EKVSYKVQAGDSI----DITVPPAKPLSLEAQNLNLDIVYEDADVIVVNKPQGMVVHPSAGHPDHTLVNGL--LYHTHELADSPEGFRPGIVHRIDKDTSGLLMVAKNDKARESLEKQLAEKINKREYLAIVHGNFETKNGVIDAPIGR-NPNNRKQMAVNPKGKAAVTHFTVLEQFKDYSLVKCILETGRTHQIRVHMKYIGHPLAGDPLYGPK--KTLAGHGQFLHAKTLGFYQPSTHKWLEFSAPLPAIFEKQLE 296
>gi|126695551|ref|YP_001090437.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9301] >gi|126542594|gb|ABO16836.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9301] (319 aa)
Score = 340, Expect = 3.9e-30, Identities = 97/288 (33%), Positives = 156/288 (54%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETST-RREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD  LVS +   SR+  +H I + LV VN K   +K   K  +  +I +      E    L P K D+ I++ED++I+++NK + +IVHP   + S TL N +  +F  K +      LR GIVHRLDK T G ++VAKS ++     K   ++   ++Y+A++H    +   ++   I R + +  + +V  +   + ART +K   ++ N++L   +L TGRTHQIRVH   I + ++ DP+YG          GQ L A KL  IHP   KE+    ++P +F++ +
  S:    28 RLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPP---EPLIYLKPEKMDLNILFEDEHIIVINKQSGLIVHPAPGNKSGTLVNGL--LFHCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAPNSEEGQIVGHIGRDKLNRLKYKVVEETSGRYARTYWKLEERFGNYSLMSFKLDTGRTHQIRVHCAHINHPIVGDPLYGRCKKLPCKLDGQALHAIKLGLIHPINGKEMIFESELPLDFQKLL 313
>gi|167627646|ref|YP_001678146.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017] >gi|167597647|gb|ABZ87645.1| Lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017] (328 aa)
Score = 340, Expect = 4.1e-30, Identities = 104/284 (36%), Positives = 167/284 (58%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV-DEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPL-RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +R+D  ++  F   SRS  +  I++ L+TVNGK     +  + DEE EI ++     E + E+         D+ IV+ED  I++++KP D++VHP + +++ T++N + + +       N D L R GIVHRLDK T GL++ AKS  +++   +   ++K+ +KYLA++   +      ++ PI R + + R +++ +   KEA T +K I  Y  FTL E +L TGRTHQIRVH + IK+ ++ D  Y  K   K  K G      Q L AYKL F+HP +QK V     +P++
  S:    23 KRIDSTINELFEQFSRSQIQKWIKDGLITVNGKTTKSKHILLGDEEVEINIELLPTNEWLAEDI--------DLNIVFEDNDIIVIDKPIDMVVHPGAGNMTGTISNALLHKYP------NQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLSERKVSRKYLAIVEGEIYEEGT-INQPIGR-DLNNRTKMTINHKGKEAITHYKPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYN-KSSTKLDKVGIENINRQALHAYKLSFMHPTSQKIVRFKSKLPED 302
>gi|148269598|ref|YP_001244058.1| RluA family pseudouridine synthase [Thermotoga petrophila RKU-1] >gi|147735142|gb|ABQ46482.1| ribosomal large subunit pseudouridine synthase D [Thermotoga petrophila RKU-1] (311 aa)
Score = 340, Expect = 4.1e-30, Identities = 102/290 (35%), Positives = 166/290 (57%)
  Q:     6 RLDILVSSKFS--LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNF-TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  +  K    +SRS+ +  I+   V VNG+I  KP+ K+ +E EI+  +     +   + P + +++++YED+ I++++KP D+IVHP    LS TL N +  +   K ++  G  LR GIVHRLDK T G+++VAK+  +  + +K F D+K++K Y+ L+   ++     VD P+ R     R +++     KEA T ++ + ++ +  TL      TGRTHQIRVH + + + ++ D IYG PK         Q L A KL F HP T K +     +P++FKE I++
  S:    14 RLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQI-KKPSYKL-KEGEIVEVDLPEKPQEATVQPEEIELKVLYEDRDIVVIDKPGDMIVHPVPSKLSGTLVNAL--LNHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYILLVKGRVKKDEGVVDLPLAR-HPVLRIKMAVVETGKEAITEYRVLKRFDDVATLVLAFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEIFGIKRQMLHALKLGFFHPRTGKWMEFVSPLPEDFKEAIRR 302
>gi|73749059|ref|YP_308298.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides sp. CBDB1] >gi|73660775|emb|CAI83382.1| ribosomal large subunit pseudouridine synthase,RluD subfamily [Dehalococcoides sp. CBDB1] (300 aa)
Score = 340, Expect = 4.3e-30, Identities = 96/290 (33%), Positives = 159/290 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +RLD  ++ K S LSRS  +  + +  + VN +  +KP+ ++     I +  E   E    L      +EI+++DK +L++NKP  + VHP      +TL N +  +    +++   DPLR GIVHRLDK T GL++VAK+  +    +  F ++ I K YLAL+   L+     ++AP+ R +   R++++   D + ART +K +   + ++L EV+L TGRTHQIRVH   I + V  D +YG K   ++    Q+L A++L F  P   + V     +P + +E +K
  S:    13 ERLDKYITQKESGLSRSFIQELVSSGHILVNNQS-AKPSLRLKTGDTITI--EIPPETPSELKAEDIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLAL--EPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTIRKYYLALVKGELRPAEGFIEAPLGR-DPQNRQKIAVVSDGRHARTGYKVLRYIQGYSLLEVKLETGRTHQIRVHFAAIGHPVAGDAVYGQK---ESWVKRQFLHAHRLSFALPSNGQVVEFTSPLPPDLEEALK 294
>gi|110803816|ref|YP_699133.1| pseudouridine synthase [Clostridium perfringens SM101] >gi|110684317|gb|ABG87687.1| pseudouridine synthase [Clostridium perfringens SM101] (306 aa)
Score = 339, Expect = 4.4e-30, Identities = 80/226 (35%), Positives = 131/226 (57%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           + I+YED+ +++VNKP  ++VHP   + + TL N + Y  D      NG  +R GIVHR+DK T G+++VAK+ ++     + F D  I+++Y A++    +     +DAP+ R     R + +   D K A T ++ +  + + +L +  L TGRTHQIRVH  FI + ++ D +YG K   K ++ GQ L A  L FIHP T K V  + ++P+ F++ ++K G
  S:    82 LNIIYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLYHCDDLS-GING-VIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGR-HHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLSQEGQVLHAKTLGFIHPTTGKYVEFDSELPEYFEKIVEKLG 304
>gi|15643228|ref|NP_228272.1| hypothetical protein TM0462 [Thermotoga maritima MSB8] >gi|4980971|gb|AAD35547.1|AE001724_5 conserved hypothetical protein [Thermotoga maritima MSB8] (311 aa)
Score = 339, Expect = 5.0e-30, Identities = 100/290 (34%), Positives = 166/290 (57%)
  Q:     6 RLDILVSSKFS--LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNF-TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  +  K    +SRS+ +  I+   V VNG+I  KP+ K+ +E EI+  +     +   + P + +++++YED+ I++++KP D+IVHP    LS TL N +  +   K ++  G  LR GIVHRLDK T G+++VAK+  +  + +K F D+K++K Y+ L+   ++     +D P+ R     R +++     KEA T ++ + ++ +  TL      TGRTHQIRVH + + + ++ D IYG PK         Q L A KL F HP T + +     +P++FKE I++
  S:    14 RLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQI-KKPSYKL-KEGEIVEVDLPEKPQEATVQPEEIELKVLYEDRDIIVIDKPGDMIVHPVPSKLSGTLVNAL--LHHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYILLVKGKMKNDEGVIDLPLAR-HPVLRIKMAVVETGKEAITEYRVLKRFDDVATLVLAFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEIFGIKRQMLHALKLGFFHPRTGEWMEFVSPLPEDFKEAIRR 302
>gi|114566812|ref|YP_753966.1| pseudouridylate synthase [Syntrophomonas wolfei subsp. wolfei str. Goettingen] >gi|114337747|gb|ABI68595.1| ribosomal large subunit pseudouridine synthase D [Syntrophomonas wolfei subsp. wolfei str. Goettingen] (305 aa)
Score = 339, Expect = 5.0e-30, Identities = 96/286 (33%), Positives = 157/286 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP--KHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +RLD  V+ +   LSRS+ K  IEN  + V+ K   KP+ ++    EII+ E   V E K L      +  +Y+DK I +++KP  ++ HP   +  NTL N +  +F  K +      LR GIVHRLDK T G++++AK+  +         D  I ++Y+ L+H  ++     ++API R +   R++++     + A + ++ + +  N+TL +V+L TGRTHQIRVH  +IK+ V+ DP+YG   K +   T   Q L A+ L F HP + +      ++P  F+
  S:    16 ERLDAFVTEQLDELSRSLVKTLIENGEIRVDSKQ-QKPSYRLKAGEEIIV-EIPAVRELK-LKAQDIPLSFIYQDKDIAVIDKPKGMVAHPAHGNWENTLVNAL--LFHLKDLSGINGELRPGIVHRLDKDTSGVMVIAKNDMAHRQLAAQIKDHSINREYITLVHGIIKENLGSIEAPIGRSKQD-RKKMAVIAGGRPAVSNYQVLERLGNYTLLKVKLLTGRTHQIRVHFAYIKHPVVGDPLYGSGKKQLGLDT---QALHAHLLGFKHPSSGEYREFKSELPLYFE 295
>gi|147669825|ref|YP_001214643.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides sp. BAV1] >gi|146270773|gb|ABQ17765.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides sp. BAV1] (300 aa)
Score = 339, Expect = 5.1e-30, Identities = 95/290 (32%), Positives = 159/290 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +RLD  ++ K S LSRS  +  + +  + VN +  +KP+ ++     I +  E   E    L      +EI+++DK +L++NKP  + VHP      +TL N +  +    +++   DPLR GIVHRLDK T GL++VAK+  +    +  F ++ + K YLAL+   L+     ++AP+ R +   R++++   D + ART +K +   + ++L EV+L TGRTHQIRVH   I + V  D +YG K   ++    Q+L A++L F  P   + V     +P + +E +K
  S:    13 ERLDKYITQKESGLSRSFIQELVSSGHILVNNQS-AKPSLRLKTGDTITI--EIPPETPSELKAENIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLAL--EPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTVRKYYLALVKGELRPAEGFIEAPLGR-DPQNRQKIAVVSDGRHARTGYKVLRYIQGYSLLEVKLETGRTHQIRVHFAAIGHPVAGDAVYGQK---ESWVKRQFLHAHRLSFALPSNGQVVEFTSPLPPDLEEALK 294
>gi|82545047|ref|YP_408994.1| 23S rRNA pseudouridine synthase D [Shigella boydii Sb227] >gi|187732689|ref|YP_001881382.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii CDC 3083-94] >gi|81246458|gb|ABB67166.1| suppressor of ftsH mutation [Shigella boydii Sb227] >gi|187429681|gb|ACD08955.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii CDC 3083-94] (326 aa)
Score = 339, Expect = 5.4e-30, Identities = 101/290 (34%), Positives = 157/290 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +L  T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNLDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPEDMVELIE 310
>gi|15603584|ref|NP_246658.1| 23S rRNA pseudouridine synthase D [Pasteurella multocida subsp. multocida str. Pm70] >gi|20139708|sp|Q9CKA6|RLUD_PASMU Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|12722131|gb|AAK03803.1| SfB [Pasteurella multocida subsp. multocida str. Pm70] (324 aa)
Score = 339, Expect = 5.5e-30, Identities = 99/290 (34%), Positives = 160/290 (55%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  IE NLV VNG +++ P  KV   E+ EI+++    +++     P    + IVYED  IL++NKP D +VHP + + S T+ N + Y + +       +  R GIVHRLDK T GL+++AK++ +     +    +KI ++Y A+    + T+   VD P+ R  T  R  ++     K A T ++ + +++N+T   + L TGRTHQIRVH   I + ++ D  YG     PK+ ++           Q L A  L+  HP T + +  +  +P +F E ++
  S:    17 QRLDQALAELFPDYSRSRLKTWIEQNLVHVNGDVVNVPRAKVYGGEQIEIVVE----IDDDTRFEPENLPLNIVYEDDDILVINKPKDFVVHPGAGNASGTVLNALLYHYPAI-----AEVPRAGIVHRLDKDTTGLMVIAKTIPAQTKLVRDLQKRKITREYEAIACG-IMTKGGMVDQPMARHPTK-RTHMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEELMQTLRDFKRQALHAIMLRLAHPITGELMEWHAPLPTDFVELVE 309
>gi|94987255|ref|YP_595188.1| pseudouridylate synthases, 23S RNA-specific [Lawsonia intracellularis PHE/MN1-00] >gi|94731504|emb|CAJ54867.1| Pseudouridylate synthases, 23S RNA-specific [Lawsonia intracellularis PHE/MN1-00] (541 aa)
Score = 338, Expect = 5.8e-30, Identities = 94/273 (34%), Positives = 160/273 (58%)
  Q:    17 LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN--FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           +SR   K  I +    ++ K+   P+T++     I ++  ++V     L P +  +EI++ D+++ I+NKP  + VHP      +TL + ++KY    K I+  G  LR GIVHR+DK T GL+ +A + D+    +K+FLD+KI K+YLAL+H  + +    +  P+ R +  T+ +V+ +   K A T ++ +++ KN  +++  + + TGRTHQIRVH + I + ++ D +Y   H+NKT +   Q L A+KL F HP T K++N     PK+F
  S:    31 VSRERLKKVIVSGGCKIDDKVCFSPSTRLKVGMHIFIQLPEVVS---ALLPEEGFLEILFSDEHLAIINKPPGLTVHPAPSCQESTLVHRLLKYF--PKLIEQGG--LRPGIVHRIDKDTSGLLCIALTEDTRLKLSKIFLDRKINKEYLALVHG-VPSMEGYIAVPLGR-DPKTKVKVAVNPKGKPAHTEWRVLHRGKNDVYSILALTIQTGRTHQIRVHMKHIGHPLVGDKLYAGGHVNKTFQCNRQMLHAWKLSFEHPITGKKMNFLCPPPKDF 298
>gi|153814897|ref|ZP_01967565.1| hypothetical protein RUMTOR_01112 [Ruminococcus torques ATCC 27756] >gi|145847928|gb|EDK24846.1| hypothetical protein RUMTOR_01112 [Ruminococcus torques ATCC 27756] (303 aa)
Score = 338, Expect = 6.4e-30, Identities = 94/294 (31%), Positives = 159/294 (54%)
  Q:     2 KNTQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLT--PWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           ++ +R+D  +S    +LSRS  +  +++  ++VN   + KPN K+ E  +I    E  + + +VL   P    ++I+YED  ILIVNKP +++VHP      +TL N + Y         NG  LR GIVHR+D  T G +++ K+  +     +   +  I ++Y A++H  ++     V+API R     ++  ++  + K A T +  + ++K++T  E EL TGRTHQIRVH   I + ++ D +YGP       + GQ L A  L   HP T K + ++  +P+ F + +K+
  S:    10 RSGERIDRFLSENLENLSRSYIQKLLKDGKISVNQSSV-KPNYKISENDKI----EVFIPDPEVLDILPENIPLDILYEDSDILIVNKPKNMVVHPAPGHYEHTLVNAVMYHCKDNLSGING-ILRPGIVHRIDMDTTGSLLICKNDKAHQIIAEQLKEHSITRRYHAIVHGKIKEDNGVVNAPIGRHPIDRKKMSTKAKNGKHAVTHYTVLRRFKDYTYIECELETGRTHQIRVHMASIGHPILGDSMYGPSKCPFKLQ-GQTLHAKVLGITHPSTGKYIEVDAPLPEYFNKLLKQ 299
>gi|168215478|ref|ZP_02641103.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC 8239] >gi|182382386|gb|EDT79865.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC 8239] (306 aa)
Score = 337, Expect = 8.3e-30, Identities = 80/226 (35%), Positives = 131/226 (57%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           + IVYED+ +++VNKP  ++VHP   + + TL N + Y  D      NG  +R GIVHR+DK T G+++VAK+ ++     + F D  I+++Y A++    +     +DAP+ R     R + +   D K A T ++ +  + + +L +  L TGRTHQIRVH  FI + ++ D +YG K   K ++ GQ L A  L FIHP T + V  + ++P+ F++ ++K G
  S:    82 LNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLYHCDDLS-GING-VIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGR-HHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLSQEGQVLHAKTLGFIHPTTGEYVEFDSELPEYFEKIVEKLG 304
>gi|194246668|ref|YP_002004307.1| Pseudouridine synthase [Candidatus Phytoplasma mali] >gi|193807025|emb|CAP18461.1| Pseudouridine synthase [Candidatus Phytoplasma mali] (299 aa)
Score = 337, Expect = 8.8e-30, Identities = 100/290 (34%), Positives = 166/290 (57%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVE------ETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  ++ K + S++  +  I    + VN    +KP+ K       ILKE   ++         VL P   ++EI+YED+++ +++KP ++++HP+      TL N +  +F  K  +   D LR GIVHRLDK T GL++VAKS +           ++I++ Y AL+H HL+ +  ++  PI R     R +++   + K + T FK +  + NF+L E +L TGRTHQIRVH  ++K+H++ D +YG K  N  +   Q+L + K++FIHP T+K + +   +P  F+  +KK
  S:    15 RLDHFLNKKINFSKNRCQKLIILGKILVN----NKPSKK-----SYILKENDHIKVFIPSTPLNVLQPIDLNLEIIYEDEFLAVIDKPKNLVIHPSITFSGVTLINGL--LFQIKNFR-KMDGLRPGIVHRLDKDTTGLILVAKSEEIRQQLQLSIQKREIKRYYWALIHGHLEKQG-KIILPIGR-HPHNRIKMAVVKNGKPSITYFKVLKYFNNFSLIECQLETGRTHQIRVHLSYLKHHILGDKLYGLKE-NCYSNESQFLHSKKIEFIHPITKKNIFLESILPIGFQNVVKK 295
>gi|193216796|ref|YP_002000038.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma arthritidis 158L3-1] >gi|193002119|gb|ACF07334.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma arthritidis 158L3-1] (298 aa)
Score = 337, Expect = 9.1e-30, Identities = 96/268 (35%), Positives = 153/268 (57%)
  Q:     4 TQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY-----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFI 271
           ++R+D  +++   ++R+  +  I    V VN   I+K    V E  EI +   K++++ + +      +EIVYE    L++NKP+ ++VHP     S TL N + Y F +     NG  LRMGIVHR+DK T GL++VAK+ ++ N F KL  + +I++ Y A++  H++ R + +D PI R   + ++    + ++KEA T   E+ KY     +N TL +  L TGRTHQIRVH  +IK+ V  DP+Y      K   + Q L A +L F+
  S:     9 SERIDKYIANNSEITRNDIQALIVQGAVFVNSTKINKNKYIVHENDEIEII--KLLDKQQNIEAQNLPLEIVYECDDYLVINKPSGLVVHPAPGHSSGTLVNSLMYHFKNNLSDVNG-LLRMGIVHRIDKDTSGLLLVAKNNETHNYFAKLLKNHEIKRTYYAIVDGHIENRLINLDLPIGRDPNNRQKFAVTEQNSKEAFTAL-EVIKYLNLAGQNKTLVKCNLKTGRTHQIRVHLAYIKHPVYGDPVYN----KKVDDFNQRLHAKELDFV 273
>gi|118475501|ref|YP_892378.1| ribosomal pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40] >gi|118414727|gb|ABK83147.1| ribosomal pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40] (323 aa)
Score = 337, Expect = 9.4e-30, Identities = 101/293 (34%), Positives = 156/293 (53%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIK---YIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           N+ RLD +++S  S+SR+     I++  V VN  ++ KP+ KV    +I     K   E         D+EI+YED  IL++NKP+++ VHP       TL   +K   Y+  +     NGD +R GIVHRLDK T G+++VAK+  S +A      D+ + + YLAL+  +L+ + + +D PI R     R + S   + + A++ F  I    +  L   +LFTGRTHQIRVH   I  H++ D +YG K  N   K    L AY L   HP + +++     +P +F + + K
  S:     8 NSARLDQILASYLSISRNQISELIKSGNVYVNDNLMLKPSFKVLLNDKIGFNLPKAKFENCEFKA-DFDVEILYEDDDILVLNKPSNLTVHPAPSVKEATLVEWLKQNGYMLST----LNGD-IRAGIVHRLDKGTSGVIVVAKNNASHSALAAQLSDKSMGRVYLALIDFNLKDKLI-IDRPIGR-NPQNRLKNSVAANGRAAKSAFTNIICEDDLNLIAAKLFTGRTHQIRVHLASINRHILGDNLYGFKSKNCKIKR-VMLHAYILNLTHPKSGEKMQFIAPLPTDFYDILSK 294
>gi|121607091|ref|YP_994898.1| RluA family pseudouridine synthase [Verminephrobacter eiseniae EF01-2] >gi|121551731|gb|ABM55880.1| ribosomal large subunit pseudouridine synthase D [Verminephrobacter eiseniae EF01-2] (344 aa)
Score = 336, Expect = 9.7e-30, Identities = 89/296 (30%), Positives = 157/296 (53%)
  Q:     2 KNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPL---RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQ-TRTVEVDAPIKRVETSTRREVSRDI---DAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           ++  R+D  LV      SRS  +  +    V++NG+ + K  ++V+    ++L+    V+ ++   P   DI++VYED ++L++NKP  ++VHP     S TL N +        +  + + L   R GIVHRLDK T GL++VA+   + +A       ++++++YLAL H      R+  V API R   +  R    D+     K ART    ++        +  L TGRTHQIRVH   +++ ++ D +YG   +    +  Q L A +L F+HP T + +  + ++P++ ++ +  +G
  S:    46 QHAARIDRALVELVPEFSRSYLQQLLAQGGVSLNGRPVRKAASRVNAGDRVVLEMRPTVQ-SQAFRPQPMDIDVVYEDAHLLVLNKPAGLVVHPAPGHWSATLLNGL--------LARDANALLLPRAGIVHRLDKDTSGLMVVARDRATMDALVAQIARRQVQRQYLALAHGAWSGPRSRSVQAPIGRDPRNRLRMAVVDLARHAGKCARTDVLCLDATPQGCWLQCRLHTGRTHQIRVHMASLQHPLVGDGLYGGAPLGALQR--QALHAERLAFVHPATGQALQFHAEVPQDMQQALSSWG 338
>gi|21672662|ref|NP_660729.1| ribosomal large subunit pseudouridine synthase D [Buchnera aphidicola str. Sg (Schizaphis graminum)] >gi|25009121|sp|Q8K9E9|RLUD_BUCAP Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|21623299|gb|AAM67940.1| ribosomal large subunit pseudouridine synthase d [Buchnera aphidicola str. Sg (Schizaphis graminum)] (315 aa)
Score = 336, Expect = 9.9e-30, Identities = 108/291 (37%), Positives = 168/291 (57%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIV-----EETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----------PKHI-NKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE---YIKK 295
           +RLD ++S  F   SRS  K  I  N V +NGKI ++P+ K       IL  EKI      E+  +  P    +  +YED  ILI+NKP  ++VHP + +   T+ N + Y + +     +  P R GI+HRLDK T GL+++AK++ S+N    L   +KI +KY  ++  ++ +  + V+ PI R     R  ++ D   K++ T +K IN++K  T     L TGRTHQIRVH   I   ++ DP+YG            ++I  K   + Q L A  ++FIHPFTQK ++ +  +P++ K+   Y+KK
  S:    18 KRLDQILSKLFMQYSRSCLKKWIIMNNVYINGKIENQPDKK-------ILGGEKITIYSTDEKLPINLPQNIALNTIYEDSNILIINKPPGLVVHPGAGNQDGTILNALLYRYTN----ISSIP-RCGIIHRLDKDTSGLMVIAKTIFSYNKLVTLLKKRKIIRKYQGIIKGNMISGGI-VNYPIMR-HPFKRICMTTDSLGKKSITHYKIINRFKFHTHVSFRLETGRTHQIRVHMLHIGYPLLGDPLYGGIDYGCNYFQENRNIYRKFNLFRQALHADYIEFIHPFTQKVMSWSASLPQDMKDILLYLKK 315
>gi|167750498|ref|ZP_02422625.1| hypothetical protein EUBSIR_01474 [Eubacterium siraeum DSM 15702] >gi|167656424|gb|EDS00554.1| hypothetical protein EUBSIR_01474 [Eubacterium siraeum DSM 15702] (303 aa)
Score = 336, Expect = 1.0e-29, Identities = 96/277 (34%), Positives = 147/277 (53%)
  Q:    17 LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           ++RS A   IE     VNGKI +K N K+     + L   +   +   + P    ++IVYED  +L+VNKP  ++VHP     S TL N + Y         NG  +R GIVHR+D+ T GL+IVAK+  + N   +        ++Y+A++   ++     VDAPI R +T  ++      +++EA T +     Y+N TL  + L TGRTHQIRVH  +I + V  D +YG    N + K+  GQ L A K+ FIHP   + +  + ++P  FK+ +
  S:    25 ITRSAAAALIEQGCCLVNGKIAAK-NQKLKTGDTVTLDVPE--AQPADILPENIPLDIVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNALMYHCGDSLSGING-VIRPGIVHRIDRDTSGLLIVAKNDTAHNILAEQIKVHSFTREYMAVVQGVIKEDGT-VDAPIGRHKTDRKKMCVTTENSREAVTHYFVEQTYRNNTLVRLRLETGRTHQIRVHMAYIGHPVTGDEVYG----NGSPKWLCGQCLHAKKIGFIHP-DGRYMEFDSELPDYFKKLL 293
>gi|150020881|ref|YP_001306235.1| RluA family pseudouridine synthase [Thermosipho melanesiensis BI429] >gi|149793402|gb|ABR30850.1| pseudouridine synthase, RluA family [Thermosipho melanesiensis BI429] (306 aa)
Score = 336, Expect = 1.1e-29, Identities = 99/289 (34%), Positives = 161/289 (55%)
  Q:     6 RLDILVSSKFS--LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD  +  K    +SR+  +  I++ +VTVN +   KP+ K+     +  +  +  ++ ++L P    ++I+YEDK I++VNK   ++ HPT   LS TL N + Y       +  G  LR GIVHRLDK T G+++VAK+  +  + +  F ++K EK Y+A++   ++     +D P+ R     R +++     K A T FK I ++KN TL      TGRTHQIRVH ++I + ++ D +YG     K   +G   Q L A KL F HP T +++     +P++FK+ I+
  S:    14 RLDKFIQEKAPDWISRTYIQRAIKSGMVTVNNEE-KKPSYKLKNGDVVSFELPEEPKKVEIL-PENLPLKIIYEDKDIIVVNKDPGVVTHPTPTFLSGTLVNALMY--HCNDFQGIGGELRPGIVHRLDKDTSGVIVVAKNDKAHQSLSMQFKERKTEKTYIAIVSGEVKKNYGTIDVPLGR-NPVVRTKIAPVDWGKNAITYFKVIKRFKNATLLLAFPKTGRTHQIRVHMKYIGHPLLGDELYGRG--KKDEIFGVKRQMLHALKLSFYHPSTNEKMIFVAPLPEDFKQVIR 300
>gi|120603012|ref|YP_967412.1| RluA family pseudouridine synthase [Desulfovibrio vulgaris subsp. vulgaris DP4] >gi|120563241|gb|ABM28985.1| pseudouridine synthase, RluA family [Desulfovibrio vulgaris subsp. vulgaris DP4] (541 aa)
Score = 336, Expect = 1.1e-29, Identities = 94/291 (32%), Positives = 156/291 (53%)
  Q:     1 MKNTQRLDILVSSKFS---LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVET-STRREVSRDIDAKEARTIFKEINKYK--NFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG----QYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           M+N +RLD  +    S   LSR   K  I +   TV+G + + P+T++     +   E  I      + P + D+ I++ D+++L+++KP  + VHP       TL + + + FD+ + +   +  R GIVHR+DK T GL++VA S       ++ F ++ +EK+YLAL+H  +   T EVDAPI R  T   R  V +    K AR+ ++ ++     ++ L  V + +GRTHQIRVH       +  D +YGP    +  + G    Q L A++L F HP T + +      P++F +
  S:    23 MRN-ERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRV---ELAIAPAATAVEPEEGDLTIIHRDEHLLVIDKPAGLTVHPCPSCPEGTLVHRLVHHFDALRAQ---EGFRPGIVHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEKEYLALVHG-VPPATGEVDAPIGRHPTHKVRMAVVK--GGKPARSEWRVLHAAPEGHYALVAVRIHSGRTHQIRVHMAHAGFPLWGDQLYGPGTPARLREQGYGARQMLHAWRLAFTHPVTGERLRFTCPPPQDFPD 313
>gi|182625703|ref|ZP_02953472.1| pseudouridine synthase, RluA family [Clostridium perfringens D str. JGS1721] >gi|177909105|gb|EDT71580.1| pseudouridine synthase, RluA family [Clostridium perfringens D str. JGS1721] (306 aa)
Score = 336, Expect = 1.2e-29, Identities = 80/226 (35%), Positives = 131/226 (57%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           + IVYED+ +++VNKP  ++VHP   + + TL N + +  D      NG  +R GIVHR+DK T G+++VAK+ ++     + F D  I+++Y A++    +     +DAP+ R     R + +   D K A T ++ +  + + +L +  L TGRTHQIRVH  FI + ++ D +YG K   K ++ GQ L A  L FIHP T + V  + ++P+ FK+ ++K G
  S:    82 LNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCDDLS-GING-VIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGR-HHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLSQEGQVLHAKTLGFIHPTTGEYVEFDSELPEYFKKIVEKLG 304
>gi|89901092|ref|YP_523563.1| pseudouridine synthase, RluD [Rhodoferax ferrireducens T118] >gi|89345829|gb|ABD70032.1| ribosomal large subunit pseudouridine synthase D [Rhodoferax ferrireducens T118] (334 aa)
Score = 335, Expect = 1.4e-29, Identities = 93/297 (31%), Positives = 156/297 (52%)
  Q:     1 MKNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQ-TRTVEVDAPIKRVETSTRREVSRDI---DAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +++ QRLD  LV      SRS  +  I+   VT+NG +I KP+T+V + +++   E +   +++   P    + +V+ED++++++NKP  ++VHP   + S TL N +    D+K +       R GIVHRLDK T GL++VA++    +A  +    +++ ++Y+AL H      R VE++API R   +  R    D+     K ART  + +            L TGRTHQIRVH   I + ++ D +YG +      +  Q L A +L F HP T + +     +P +    +  +G
  S:    35 VQHGQRLDRALVELVPEFSRSYLQQLIDLGGVTINGIVIHKPSTRV-KAADVGTIELRPTPQSQAFKPETMALNVVFEDEHLMVINKPAGLVVHPAPGNWSGTLLNGL-LARDAKAMNLP----RAGIVHRLDKDTSGLMVVARTRPVMDALIRSIAAREVSRQYVALAHGPWTGNRRVEINAPIGRDPRNRLRMAVVDLARNPGKLARTDVELLQNCDQGCWVLCTLHTGRTHQIRVHMAMIGHPLVADVLYGGRAEAGMQR--QALHACRLAFTHPVTLESMVFQASLPVDLNLALANWG 328
>gi|23098941|ref|NP_692407.1| hypothetical protein OB1486 [Oceanobacillus iheyensis HTE831] >gi|22777169|dbj|BAC13442.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831] (303 aa)
Score = 335, Expect = 1.6e-29, Identities = 97/290 (33%), Positives = 164/290 (56%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETK--VLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE---YIKK 295
           R+D L++   +  SRS  +  I+  LV VNG +  K N K  E   +  +    + ETK  +L P    +++VYED  ++++NKP  ++VHP++   + TL + + Y  D      NG   R GIVHR+DK T GL++VAK+  +    +     +++++KY+A++H  +   T  +DAPI R +   R++++   + K A T F+ I ++ ++T  E +L TGRTHQIRVH ++I   ++ DP Y  +        GQ L A ++ F HP T + +  + + P+ F E   +I+K
  S:    16 RVDKLLTQLLADQSRSQIQGWIDEGLVEVNG-VSVKANYKCVEGDALTWE----IPETKPLILEPENIPLDVVYEDSDVIVINKPKGMVVHPSAGHQTGTLVHALLYHCDDLS-GINGIE-RPGIVHRIDKDTSGLLVVAKNDVAHQKLSDQLQQKQLKRKYVAIVHGEIGHDTGLIDAPIGR-DPKDRQKMAVVDNGKSAITHFRVIERFPDYTFVECQLETGRTHQIRVHMQYIGFPLVGDPKYSQRKTMNVD--GQALHAKEIGFYHPKTGEWLEFDANPPEIFTEALSFIRK 301
>gi|149182321|ref|ZP_01860799.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp. SG-1] >gi|148849940|gb|EDL64112.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp. SG-1] (303 aa)
Score = 335, Expect = 1.6e-29, Identities = 103/290 (35%), Positives = 162/290 (55%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD +L   +   SRS  +  I++  V VNG  + K N K   E +II+   +  EE  V+ P   D++I +ED  +++VNKP  ++VHP     S TL N ++ +  D   I  NG  LR GIVHR+DK T GL++VAK+  +     +  +++ + +KY A++H  +      +DAP+ R +   R+ ++     ++A T F  + ++ +FT  E +L TGRTHQIRVH ++I   +  DP YGP+   KT    GQ L A  L FIHP T + +    + P+ F+  ++K
  S:    16 RLDKVLTQLEEKWSRSQVQQWIKDGNVKVNGSQV-KTNYKCAIEDKIIISIPE-PEELDVV-PENMDLDIYFEDADVIVVNKPRGMVVHPAPGHPSGTLVNGLMAHCKDLSGI--NG-VLRPGIVHRIDKDTSGLLMVAKNDLAHEKLVEQLVNKTVTRKYKAIVHGIIPHDHGTIDAPLGR-DPKDRQNMAVVDSGRDAVTHFNVLERFTDFTYVECKLETGRTHQIRVHMKYIGYPLAGDPKYGPR---KTLDLGGQALHAAVLGFIHPRTGEYLEFEAEPPEVFRHTLQK 298
>gi|95929105|ref|ZP_01311850.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684] >gi|95135006|gb|EAT16660.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684] (350 aa)
Score = 335, Expect = 1.6e-29, Identities = 98/293 (33%), Positives = 156/293 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY--KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---------------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI----KKYG 297
           +RLD  ++ +   L+RS  K  +++ LV VN + + K   K+   E   + L + + VE      P    + ++YED  ++++NK   ++VHP +   S TL N +  ++    +   G  LR GIVHRLDK T G+++  K+  + N     F D  I+++Y+AL+H  +Q     +DAPI R  T  ++  S+    + A T +K + +Y     +L E+ L TGRTHQIRVH   +   ++ DP+YG    N+T   G               Q L A  L FIHP T   +    D+P +    +     KYG
  S:    16 ERLDRFLTRQLPELTRSQLKKLVDDGLVRVNDQTV-KAGAKLRGGETVCVTLPQAQSVETL----PEDLPLTVLYEDSDLIVINKAAGMVVHPAAGHSSGTLVNAL--LYHCHDLSGVGGELRPGIVHRLDKDTSGVMVATKNDVTHNHLAAQFKDHSIQRRYVALVHGQVQNARGTIDAPIGRHPTHRKKMTSKGRGGRRAVTHWKVLRRYDADRLSLLEMRLETGRTHQIRVHLSEMNLPLVGDPLYG----NRTRANGINDLEVRNRVHALHRQALHARLLGFIHPRTGDYLEFTSDLPGDLASIVAFLDDKYG 321
>gi|42519111|ref|NP_965041.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus johnsonii NCC 533] >gi|41583398|gb|AAS09007.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus johnsonii NCC 533] (304 aa)
Score = 334, Expect = 1.6e-29, Identities = 91/289 (31%), Positives = 169/289 (58%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD +++ K + LSR+  K  + +  + VN K   K + KV     I    +  +   K L+   +++  +IVYED  +++VNKP  ++VHP++    +TL N +  ++ ++ +  + +  R GIVHR+DK T GL+++AK+  +  +  K   ++  +++YLA++H + + +   ++API R   + R++++ +   K A T F  + ++KN++L +  L TGRTHQIRVH ++I + +  DP+YGPK     + +GQ+L A  L F  P T + +  +  +P  F++ +K
  S:    15 RLDKVIAEKITDLSRTKIKELVNDKNILVNNKA-EKVSYKVQSGDVI----DVTIPPVKPLSLEAENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVNGL--LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDKARESLEKQLAEKINKREYLAIVHGNFEVKNGVINAPIGR-NPNNRKQMAVNPKGKAAVTHFTVLEQFKNYSLVKCVLETGRTHQIRVHMKYIGHPLAGDPLYGPK--KTLSGHGQFLHAKTLGFYQPSTNEWLEFSAPLPTIFEKQLK 296
>gi|78778581|ref|YP_396693.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9312] >gi|78712080|gb|ABB49257.1| ribosomal large subunit pseudouridine synthase D [Prochlorococcus marinus str. MIT 9312] (319 aa)
Score = 334, Expect = 1.7e-29, Identities = 97/289 (33%), Positives = 155/289 (53%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETST-RREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD  LVS +   SR+  +H I + LV VN K   +K   K  +  +I +      E    L P K D+ I++EDK+I+++NK + +IVHP     S TL N +  +F  K +      LR GIVHRLDK T G ++VAKS ++     K   ++   ++Y+A++H    +   ++   I R + +  + +V  +   + A T +K   ++ N++L   +L TGRTHQIRVH   I + ++ DP+YG          GQ L A KL  IHP   KE+    ++P +F++ ++
  S:    28 RLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNVQIWMPPP---EPLIYLKPEKMDLNILFEDKHIIVINKQSGLIVHPAPGHKSGTLVNGL--LFHCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAPNSEEGQIVGHIGRDKLNRLKYKVVEETTGRYACTYWKLEERFGNYSLMSFKLDTGRTHQIRVHCAHINHPIVGDPLYGRCKKLPCQLDGQALHAIKLGLIHPINGKEMIFESELPLDFQKLLR 314
>gi|153853142|ref|ZP_01994551.1| hypothetical protein DORLON_00536 [Dorea longicatena DSM 13814] >gi|149753928|gb|EDM63859.1| hypothetical protein DORLON_00536 [Dorea longicatena DSM 13814] (272 aa)
Score = 334, Expect = 1.7e-29, Identities = 86/270 (31%), Positives = 147/270 (54%)
  Q:    26 IENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           ++   V VN K + K N ++   +  E+ L E K  +    + P    ++I+YED+ I+++NKP  ++VHP     S TL N + Y    +    NG  +R GIVHR+D  T G ++V K+  +  + ++      I + Y+A++H +++  +  V+API R  T  ++  +   + ++A T +K + ++ ++T  + EL TGRTHQIRVH   I + ++ D +YGPK        GQ L A  L  IHP T K + +N  +P+ F E + +
  S:     1 MKEGYVKVNQKPV-KSNYRLSFGDSVEVTLPEAKEPD----IVPENIPLDILYEDQDIIMINKPKQMVVHPAPGHYSGTLVNALMYHCGDELSGING-CMRPGIVHRIDMDTTGSLVVCKNDKAHQSLSEQLKVHSIRRIYVAIVHGNIKEDSGTVNAPIGRHPTDRKKMSTHCKNGRDAVTHYKVLERFGDYTYIQCELETGRTHQIRVHMASIGHPLVGDEVYGPKKCPFKGLQGQTLHARTLGIIHPTTGKYLEVNAPLPEYFIELLDR 266
>gi|194323822|ref|ZP_03057598.1| pseudouridine synthase, RluA family [Francisella tularensis subsp. novicida FTE] >gi|194322186|gb|EDX19668.1| pseudouridine synthase, RluA family [Francisella tularensis subsp. novicida FTE] (317 aa)
Score = 334, Expect = 1.8e-29, Identities = 99/284 (34%), Positives = 169/284 (59%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP-----KHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +R+D++++ +F   SR+  +  ++   +TVNG+  +KP   V  DEE EI ++     E I E+         +++I++ED  I++++KP ++IVHP + + + T++N + + + D  K+       R GIVHRLDK T GL++ AKS  +++   +   ++K+ +KYLA++   +  +   ++ PI R + + R +++ +   KEA T +  I  Y  FTL E +L TGRTHQIRVH + IK+ ++ D  Y       + +  TT   Q L AYKL FIHP T K V     +P++
  S:     8 KRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRA-TKPKHIVLGDEEVEINIELLPTNEWIAEDI--------NLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLP------RAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGT-INQPIGR-DPTNRTKMAINYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITTPTRQALHAYKLSFIHPTTAKMVKFKSKLPED 287
>gi|16130515|ref|NP_417085.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr. MG1655] >gi|89109396|ref|AP_003176.1| 23S rRNA pseudouridine synthase [Escherichia coli W3110] >gi|157162070|ref|YP_001459388.1| 23S rRNA pseudouridine synthase D [Escherichia coli HS] >gi|170019127|ref|YP_001724081.1| RluA family pseudouridine synthase [Escherichia coli ATCC 8739] >gi|170082199|ref|YP_001731519.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K12 substr. DH10B] >gi|188493998|ref|ZP_03001268.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli 53638] >gi|194439337|ref|ZP_03071415.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli 101-1] >gi|2507541|sp|P33643|RLUD_ECOLI Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|1236631|gb|AAA92957.1| SfhB >gi|1788946|gb|AAC75643.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr. MG1655] >gi|85675474|dbj|BAA16479.2| 23S rRNA pseudouridine synthase [Escherichia coli W3110] >gi|157067750|gb|ABV07005.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli HS] >gi|169754055|gb|ACA76754.1| pseudouridine synthase, RluA family [Escherichia coli ATCC 8739] >gi|169890034|gb|ACB03741.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K12 substr. DH10B] >gi|188489197|gb|EDU64300.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli 53638] >gi|194421699|gb|EDX37708.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli 101-1] (326 aa)
Score = 334, Expect = 1.8e-29, Identities = 101/290 (34%), Positives = 156/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+I+NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|154173855|ref|YP_001407891.1| ribosomal large subunit pseudouridine synthase D [Campylobacter curvus 525.92] >gi|112803415|gb|EAU00759.1| ribosomal large subunit pseudouridine synthase D [Campylobacter curvus 525.92] (323 aa)
Score = 334, Expect = 1.8e-29, Identities = 98/292 (33%), Positives = 157/292 (53%)
  Q:     4 TQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKI--KYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + RLD+ ++S+  +SR+ A + I+N LV+VN K   KP+ ++++  EI +K     E+T        +I ++YED+ IL++NKP  I+VH      S   A +++++     +    NGD LR GIVHRLDK T G ++VAK+  +  A +    D+ + + YLAL    L+   + +D PI R   S R ++    + + A++ F  + +     L   +LFTGRTHQIR H   I  H++ D +YG K  N   K    L AY L F HP + ++V        +F + + K
  S:     9 SSRLDVALASELKISRNQATNLIKNALVSVNSKPALKPSMQLNQNDEICVKFALPKEKTNDYEA-NFEIPVIYEDEDILVLNKPPQIVVHQAP---SVKEATLVEWLNQKGFMLSNLNGD-LRAGIVHRLDKGTSGAIVVAKNNAAHAALSAQLNDKSMGRIYLALTDLPLKQECI-IDKPIGR-SPSNRLKMGIVTNGRHAKSAFLNLVQTDEVNLIAAKLFTGRTHQIRAHLASINRHILGDNLYGFKSENDKIKR-VMLHAYMLYFFHPRSGEKVEFIAQTWDDFNQIVYK 294
>gi|118497849|ref|YP_898899.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. novicida U112] >gi|118423755|gb|ABK90145.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. novicida U112] >gi|151572378|gb|EDN38032.1| hypothetical protein FTDG_00834 [Francisella tularensis subsp. novicida GA99-3548] (332 aa)
Score = 334, Expect = 2.0e-29, Identities = 99/284 (34%), Positives = 169/284 (59%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP-----KHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +R+D++++ +F   SR+  +  ++   +TVNG+  +KP   V  DEE EI ++     E I E+         +++I++ED  I++++KP ++IVHP + + + T++N + + + D  K+       R GIVHRLDK T GL++ AKS  +++   +   ++K+ +KYLA++   +  +   ++ PI R + + R +++ +   KEA T +  I  Y  FTL E +L TGRTHQIRVH + IK+ ++ D  Y       + +  TT   Q L AYKL FIHP T K V     +P++
  S:    23 KRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRA-TKPKHIVLGDEEVEINIELLPTNEWIAEDI--------NLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLP------RAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGT-INQPIGR-DPTNRTKMAINYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITTPTRQALHAYKLSFIHPTTAKMVKFKSKLPED 302
>gi|49259508|pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine Synthase Rlud From Escherichia Coli >gi|118138510|pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli (325 aa)
Score = 334, Expect = 2.1e-29, Identities = 101/290 (34%), Positives = 156/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+I+NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    17 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 309
>gi|182419830|ref|ZP_02951070.1| ribosomal large subunit pseudouridine synthase, RluA family [Clostridium butyricum 5521] >gi|182376378|gb|EDT73960.1| ribosomal large subunit pseudouridine synthase, RluA family [Clostridium butyricum 5521] (301 aa)
Score = 333, Expect = 2.2e-29, Identities = 102/293 (34%), Positives = 160/293 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTI--FKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           ++++ +S++   S SI K    N++     ++I+        E E+I K +   +E++ + P K DIEI+YED+ IL+VNK   ++VHPT    S TLAN +I Y  +S      G    + +V RLD  T GL+I+AK+  S    +K   + K+ K+YLA++H  L+     +D PI R E      + R +D +  R+I  +K I KY+N +L E  L TGRTHQIRVH   I + +  D +YG     +     Q L AY L F  P T + +++  ++P++ K  I+K  K
  S:    22 KMEMGLSTRLIRSASIDKRIFVNDIPVKMNRVIN--------EGEVI-KIDLAKDESQDIAPEKMDIEIIYEDEDILVVNKKPFMVVHPTKSYQSGTLANGVINYFMES------GQNCIVRLVSRLDMNTSGLIIIAKNQFSHGMLSKEMTENKVTKRYLAVVHGILENEEGTIDRPIYRPE-GIDFGIMRIVDERGQRSITHYKVIEKYENASLVECTLETGRTHQIRVHLSSIGHPIYGDSLYGSGDEEQDLISRQALHAYSLDFRSPRTGEILSLKSNLPEDIKTLIEKIKK 301
>gi|86153072|ref|ZP_01071277.1| ribosomal pseudouridine synthase [Campylobacter jejuni subsp. jejuni HB93-13] >gi|121612140|ref|YP_001000956.1| ribosomal large subunit pseudouridine synthase A [Campylobacter jejuni subsp. jejuni 81-176] >gi|157415544|ref|YP_001482800.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni subsp. jejuni 81116] >gi|167005866|ref|ZP_02271624.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni subsp. jejuni 81-176] >gi|85843957|gb|EAQ61167.1| ribosomal pseudouridine synthase [Campylobacter jejuni subsp. jejuni HB93-13] >gi|87249616|gb|EAQ72575.1| ribosomal large subunit pseudouridine synthases, RluA family [Campylobacter jejuni subsp. jejuni 81-176] >gi|157386508|gb|ABV52823.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni subsp. jejuni 81116] (322 aa)
Score = 333, Expect = 2.4e-29, Identities = 95/290 (32%), Positives = 164/290 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYN-GDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY-----LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD+ ++ K + SR+     IE + V VN KI  K + K+     I +   K+  E K       DI+++YED+ +L++NKP++++VH  S   S   A ++ ++ + K    N G  +R G+VHRLDK T G +++AK+  +    ++   D+ + + YLAL+   L+   + V+  + R  ++  ++++ D +   +K A++ F  I K +N TL   +LFTGRTHQIR H   +  H++ D +YG K        G+Y     L AY L FIHP T++++ +   + ++FK  + K
  S:    11 RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISIASLKLCNEIKPQFEVDFDIDVLYEDEDLLVLNKPSNLVVHGAS---SVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINIVKTENLTLMAAKLFTGRTHQIRAHLASLNRHILGDSLYGYK--------GKYDCRIMLHAYFLYFIHPKTKEQIFVKAPLMEDFKNIMFK 298
>gi|24113932|ref|NP_708442.1| 23S rRNA pseudouridine synthase D [Shigella flexneri 2a str. 301] >gi|26248957|ref|NP_754997.1| 23S rRNA pseudouridine synthase D [Escherichia coli CFT073] >gi|30063991|ref|NP_838162.1| 23S rRNA pseudouridine synthase D [Shigella flexneri 2a str. 2457T] >gi|74313153|ref|YP_311572.1| 23S rRNA pseudouridine synthase D [Shigella sonnei Ss046] >gi|110642757|ref|YP_670487.1| 23S rRNA pseudouridine synthase D [Escherichia coli 536] >gi|110806535|ref|YP_690055.1| 23S rRNA pseudouridine synthase D [Shigella flexneri 5 str. 8401] >gi|191174579|ref|ZP_03036074.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli F11] >gi|54039250|sp|P65835|RLUD_SHIFL Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|54041741|sp|P65834|RLUD_ECOL6 Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|26109363|gb|AAN81565.1|AE016764_247 Ribosomal large subunit pseudouridine synthase D [Escherichia coli CFT073] >gi|24053038|gb|AAN44149.1| ftsH mutation suppressor [Shigella flexneri 2a str. 301] >gi|30042247|gb|AAP17972.1| ftsH mutation suppressor [Shigella flexneri 2a str. 2457T] >gi|73856630|gb|AAZ89337.1| suppressor of ftsH mutation [Shigella sonnei Ss046] >gi|110344349|gb|ABG70586.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli 536] >gi|110616083|gb|ABF04750.1| suppressor of ftsH mutation [Shigella flexneri 5 str. 8401] >gi|190905152|gb|EDV64796.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli F11] (326 aa)
Score = 333, Expect = 2.5e-29, Identities = 100/290 (34%), Positives = 156/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|46579437|ref|YP_010245.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA kinase [Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough] >gi|46448851|gb|AAS95504.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA kinase [Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough] (541 aa)
Score = 333, Expect = 2.6e-29, Identities = 94/291 (32%), Positives = 155/291 (53%)
  Q:     1 MKNTQRLDILVSSKFS---LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVET-STRREVSRDIDAKEARTIFKEINKYK--NFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG----QYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           M+N +RLD  +    S   LSR   K  I +   TV+G + + P+T++     +   E  I      + P + D+ I++ D+++L+++KP  + VHP       TL + + + FD+ + +   +  R GIVHR+DK T GL++VA S       ++ F ++ +EK+YLAL+H  +   T EVDAPI R  T   R  V +    K AR+ ++ ++     ++ L  V + +GRTHQIRVH       +  D +YGP    +  + G    Q L A+ L F HP T + +      P++F +
  S:    23 MRN-ERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRV---ELAIAPAATAVEPEEGDLTIIHRDEHLLVIDKPAGLTVHPCPSCPEGTLVHRLVHHFDALRAQ---EGFRPGIVHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEKEYLALVHG-VPPATGEVDAPIGRHPTHKVRMAVVK--GGKPARSEWRVLHAAPEGHYALVAVRIHSGRTHQIRVHMAHAGFPLWGDQLYGPGTPARLREQGYGARQMLHAWHLAFTHPVTGERLRFTCPPPQDFPD 313
>gi|157156608|ref|YP_001463915.1| 23S rRNA pseudouridine synthase D [Escherichia coli E24377A] >gi|191169060|ref|ZP_03030823.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli B7A] >gi|193064062|ref|ZP_03045147.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli E22] >gi|193071695|ref|ZP_03052596.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli E110019] >gi|194430158|ref|ZP_03062659.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli B171] >gi|157078638|gb|ABV18346.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli E24377A] >gi|190900901|gb|EDV60687.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli B7A] >gi|192929297|gb|EDV82906.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli E22] >gi|192954990|gb|EDV85492.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli E110019] >gi|194411783|gb|EDX28104.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli B171] (326 aa)
Score = 333, Expect = 2.6e-29, Identities = 100/290 (34%), Positives = 156/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISMLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|169824338|ref|YP_001691949.1| pseudouridylate synthase [Finegoldia magna ATCC 29328] >gi|167831143|dbj|BAG08059.1| pseudouridylate synthase [Finegoldia magna ATCC 29328] (307 aa)
Score = 333, Expect = 2.7e-29, Identities = 102/290 (35%), Positives = 164/290 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEAR---TIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD+ ++++  LSRS  +  IE+  V VN K   K N K++   +I    EK   E K +   K D+++VYED Y+ I+NK  D+IVHPT    S+TL N + Y F +     +GD  R GIVHRLDK T GL+I+AK  D+     ++  + +I K YL ++H       ++    IK   T   ++  + + + E +   + ++ ++   +++L +V++ TGRTHQIRVH  +I + ++ D +YG K   K     Q L AY L+FIHP T +++N+   +  +F   I+K
  S:    15 RLDVFLANEVELSRSEIQKFIEDKKVLVNYKP-QKKNYKLNSNDKIKFDYEK---EDKTIRAQKHDLDVVYEDDYLAIINKDKDVIVHPTETIYSDTLVNYLMYNFKNLS-DVDGD-YRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKTYLCIVHG-----KIDESGTIKEYMTRNPKDRKKMMVSDEGKLSISQYERLDYNDDYSLVKVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKK-EKILFDSQVLHAYNLQFIHPQTHEKINVIGKLKPDFMTAIEK 295
>gi|169343529|ref|ZP_02864528.1| pseudouridine synthase, RluA family [Clostridium perfringens C str. JGS1495] >gi|169298089|gb|EDS80179.1| pseudouridine synthase, RluA family [Clostridium perfringens C str. JGS1495] (306 aa)
Score = 333, Expect = 2.7e-29, Identities = 79/226 (34%), Positives = 131/226 (57%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           + IVYED+ +++VNKP  ++VHP   + + TL N + +  D      NG  +R GIVHR+DK T G+++VAK+ ++     + F D  I+++Y A++    +     +DAP+ R     R + +   D K A T ++ +  + + +L +  L TGRTHQIRVH  FI + ++ D +YG K   K ++ GQ L A  L FIHP T + V  + ++P+ F++ ++K G
  S:    82 LNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCDDLS-GING-VIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGR-HHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCNLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLSQEGQVLHAKTLGFIHPTTGEYVEFDSELPEYFEKIVEKLG 304
>gi|121604767|ref|YP_982096.1| RluA family pseudouridine synthase [Polaromonas naphthalenivorans CJ2] >gi|120593736|gb|ABM37175.1| ribosomal large subunit pseudouridine synthase D [Polaromonas naphthalenivorans CJ2] (344 aa)
Score = 333, Expect = 2.7e-29, Identities = 88/281 (31%), Positives = 145/281 (51%)
  Q:    17 LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPL-----RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQ-TRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
            SRS  +  IE+  V V G    K + KV    E+ + E +   +++   P +  ++IVYED+++++VNKP  ++VHP   + S TL N +             DP      R GIVHRLDK T GL++VA+   + +    +   + + ++Y+AL H   +  +T +V+API R   +  R    D++    K A T+   ++  +   L + +L TGRTHQIRVH  F+ + +++D +YG        +  Q L A +L F HP T   +      P + +  I  +G
  S:    61 FSRSYLQQLIEDGGVLVKGLKAIKTSAKVKAGDELTI-ELRPTPQSQAFKPEEMALDIVYEDRHLIVVNKPAGLVVHPAPGNWSGTLLNGL----------LAHDPQASFMPRAGIVHRLDKDTSGLMVVARQRQTMDQLVSMIAARTVSREYIALAHGTWEGAKTRQVEAPIGRDPRNRLRMAVVDLEKNSGKAASTVISLLDNAEKHCLVKCKLHTGRTHQIRVHMAFLGHPLVSDEVYGGAVAGSLQR--QALHACRLAFAHPVTGAAMEFKSLPPPDLEMAIAGFG 337
>gi|91211928|ref|YP_541914.1| 23S rRNA pseudouridine synthase D [Escherichia coli UTI89] >gi|91073502|gb|ABE08383.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli UTI89] (326 aa)
Score = 332, Expect = 2.8e-29, Identities = 100/290 (34%), Positives = 156/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQSLHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|196156256|ref|YP_002125745.1| ribosomal large subunit pseudouridine synthase D [Alteromonas macleodii 'Deep ecotype'] >gi|88772461|gb|EAR03747.1| ribosomal large subunit pseudouridine synthase D [Alteromonas macleodii 'Deep ecotype'] >gi|196112035|gb|ACG65751.1| ribosomal large subunit pseudouridine synthase D [Alteromonas macleodii 'Deep ecotype'] (327 aa)
Score = 332, Expect = 3.0e-29, Identities = 99/293 (33%), Positives = 166/293 (56%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD +++  F   SRS  K  I++  V VNG++I+ P  K+  +  + ++ E  V+    +T   +DI   IVYED++IL++NKP D++VHP + + S T+ N ++ +  +  K+       R GIVHRLDK T GL++VAK++ +          +++ ++Y A+    +    + VDAPI R  T       R++  K A T F+ I K++ +T   ++L TGRTHQIRVH   IK+ ++ D +YG     PK  ++           Q L A +L   HP T++ +     +P++ ++ +K   K
  S:    22 RLDQVLADLFPEYSRSKLKTWIQDGNVAVNGEVITVPRHKMQMDELVTVQAEMDVQ----VTSEAQDIALNIVYEDEHILVINKPADLVVHPGAGNPSGTVLNALLNHCPEIDKVP------RAGIVHRLDKDTTGLMVVAKTIPAQTHLVDQLQRREMSREYEAVALGTMVAGGI-VDAPIGRHATKRTHMAVREM-GKPAVTHFRVIEKFRAYTHLRLKLETGRTHQIRVHMAHIKHPLLGDQVYGGRPRLPKGASEEFIAALRGFQRQALHAAQLSLFHPETEEWMTWKAPLPQDMQDLLKAVKK 317
>gi|124006632|ref|ZP_01691464.1| pseudouridine synthase, RluD [Microscilla marina ATCC 23134] >gi|123987787|gb|EAY27478.1| pseudouridine synthase, RluD [Microscilla marina ATCC 23134] (360 aa)
Score = 332, Expect = 3.1e-29, Identities = 94/281 (33%), Positives = 151/281 (53%)
  Q:    16 SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVS--RDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           +++R+  ++ I    V VN + + KPN KV  E  II+   +   E++V+ P    I IVYED  +L+V+K   ++VHP   + + TL N + Y F +     +G P   G+VHR+DK T GL++VAKS  +     K F D  IE+ Y AL+    +     +D  + R     R   +       + A T +K +   +  +L +  L TGRTHQIR H + + + + ND  YG   I K T + +Y               L A  L F+HP TQK +  + ++PK+F++ ++K+
  S:    61 NITRNKTQNAIREGFVKVNDQEV-KPNYKVRPEDIIIISLPEPPRESEVV-PEDIPINIVYEDDDLLVVHKEAGMVVHPAYNNWTGTLVNALAYHFKNLPENRDGRP---GLVHRIDKDTSGLLVVAKSEHALQHLAKQFFDHTIERTYYALVWGEPKQEAGTIDVNLGRSLKDRRVTAAFPEGDFGRHAVTHYKVLKNLRYVSLVQCNLETGRTHQIRAHMKHLGHPLFNDATYGGDKILKGTVFSKYRAFVENCFKVMPRQALHAKSLGFVHPTTQKFIQFDSELPKDFQKAMEKW 353
>gi|18310832|ref|NP_562766.1| hypothetical protein CPE1850 [Clostridium perfringens str. 13] >gi|110801362|ref|YP_696533.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC 13124] >gi|168206096|ref|ZP_02632101.1| pseudouridine synthase, RluA family [Clostridium perfringens E str. JGS1987] >gi|168210787|ref|ZP_02636412.1| pseudouridine synthase, RluA family [Clostridium perfringens B str. ATCC 3626] >gi|18145514|dbj|BAB81556.1| conserved hypothetical protein [Clostridium perfringens str. 13] >gi|110676009|gb|ABG84996.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC 13124] >gi|170662443|gb|EDT15126.1| pseudouridine synthase, RluA family [Clostridium perfringens E str. JGS1987] >gi|170711120|gb|EDT23302.1| pseudouridine synthase, RluA family [Clostridium perfringens B str. ATCC 3626] (306 aa)
Score = 332, Expect = 3.2e-29, Identities = 79/226 (34%), Positives = 131/226 (57%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           + IVYED+ +++VNKP  ++VHP   + + TL N + +  D      NG  +R GIVHR+DK T G+++VAK+ ++     + F D  I+++Y A++    +     +DAP+ R     R + +   D K A T ++ +  + + +L +  L TGRTHQIRVH  FI + ++ D +YG K   K ++ GQ L A  L FIHP T + V  + ++P+ F++ ++K G
  S:    82 LNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCDDLS-GING-VIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGR-HHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLSQEGQVLHAKTLGFIHPTTGEYVEFDSELPEYFEKIVEKLG 304
>gi|160933118|ref|ZP_02080507.1| hypothetical protein CLOLEP_01961 [Clostridium leptum DSM 753] >gi|156868192|gb|EDO61564.1| hypothetical protein CLOLEP_01961 [Clostridium leptum DSM 753] (306 aa)
Score = 332, Expect = 3.2e-29, Identities = 91/290 (31%), Positives = 148/290 (51%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD +++ +   L+R+  +  +E   V +NGK  +K N K      + L+      E   L      ++IVYED  +L+VNKP  ++VHP   +   TL N +     +     NG  +R GIVHR+DK T GL++VAK+  +     +   +    ++Y A++   ++  +  V+API R     ++    + ++KEA T F+ I +Y  +T   + L TGRTHQIRVH  ++ + V  DP YGP+  +   K GQ L A  + F+HP   + +     +P  F   + K
  S:    17 RLDKVLAERLPDLTRTAIQRLLEEEQVLINGKPAAK-NRKGRAGDSVALRIPD--PEPLCLQAENVPLDIVYEDDDLLVVNKPQGMVVHPAPGNYQGTLVNALLAHCGNSLSGING-VIRPGIVHRIDKDTSGLLMVAKNDFAHQGLARQIKEHSFRREYEAVVAGRMKQESGVVNAPIGRHPIDRKKMAVTEKNSKEAVTYFRVIAEYPGYTHIRLRLETGRTHQIRVHMAYLGHPVAGDPAYGPRKPDLGLK-GQCLHARLIGFVHPRDGRYLEFESPLPDYFTRLLTK 302
>gi|15832711|ref|NP_311484.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. Sakai] >gi|168708101|ref|ZP_02740378.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. EC4045] >gi|168734060|ref|ZP_02766337.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. EC4115] >gi|168752065|ref|ZP_02777087.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4113] >gi|168758664|ref|ZP_02783671.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4401] >gi|168762387|ref|ZP_02787394.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4501] >gi|168771700|ref|ZP_02796707.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4486] >gi|168773478|ref|ZP_02798485.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4196] >gi|168778572|ref|ZP_02803579.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4076] >gi|168789497|ref|ZP_02814504.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC869] >gi|168801712|ref|ZP_02826719.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC508] >gi|195940189|ref|ZP_03085571.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. EC4024] >gi|34395799|sp|Q8X9F0|RLUD_ECO57 Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|13362928|dbj|BAB36880.1| suppressor of ftsH mutation [Escherichia coli O157:H7 str. Sakai] >gi|187770638|gb|EDU34482.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4196] >gi|188014009|gb|EDU52131.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4113] >gi|189003176|gb|EDU72162.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4076] >gi|189354550|gb|EDU72969.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4401] >gi|189359603|gb|EDU78022.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4486] >gi|189367297|gb|EDU85713.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC4501] >gi|189370886|gb|EDU89302.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC869] >gi|189376176|gb|EDU94592.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:H7 str. EC508] (326 aa)
Score = 332, Expect = 3.2e-29, Identities = 100/290 (34%), Positives = 156/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|169190638|ref|ZP_02850560.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2] >gi|169002725|gb|EDS49604.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2] (315 aa)
Score = 332, Expect = 3.5e-29, Identities = 94/289 (32%), Positives = 153/289 (52%)
  Q:     5 QRLDILVSSKF---SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY-KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +R+D  V+      S+SR+  +  I++  V VN   + KPN K+     + ++  +   E   +      ++IVYED  ++++NKP  ++VHP     S T+ N + Y    K +      LR GIVHR+DK T GL++ AK+  +  +  +   D  + +KY+AL+H +L      +DAPI R +   +     D ++K A T F  + +   ++T+ E++L TGRTHQIRVH ++I   +  DP+YG    NKT    GQ L A  L F HP T + +     +P + +  I
  S:    24 ERIDKFVTDSLNEDSISRTQVQEWIKSGAVLVNQNTV-KPNYKLSSGDHVGIRVPE--PEDAAIVAEDIPLDIVYEDADVIVINKPRGMVVHPAPGHSSGTVVNALMY--HCKDLSGINGVLRPGIVHRIDKDTSGLLMAAKNDLAHVSLAEQLKDHSVSRKYIALVHGNLPHDQGTIDAPIGRDQNDRKLFTVTDRNSKHAVTHFAVLERIADDYTIVELQLETGRTHQIRVHMKYIGYPLAGDPMYGR---NKTVALKGQALHAAVLGFKHPRTGEFLEFEAPIPADMEHVI 309
>gi|117624818|ref|YP_853731.1| 23S rRNA pseudouridine synthase D [Escherichia coli APEC O1] >gi|115513942|gb|ABJ02017.1| 23S rRNA pseudouridine synthase [Escherichia coli APEC O1] (326 aa)
Score = 331, Expect = 3.7e-29, Identities = 100/290 (34%), Positives = 156/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQMAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQSLHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|170683711|ref|YP_001744779.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli SMS-3-5] >gi|170521429|gb|ACB19607.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli SMS-3-5] (326 aa)
Score = 331, Expect = 3.8e-29, Identities = 100/290 (34%), Positives = 155/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED  I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|91783470|ref|YP_558676.1| ribosomal large subunit pseudouridine synthase D [Burkholderia xenovorans LB400] >gi|91687424|gb|ABE30624.1| ribosomal large subunit pseudouridine synthase D [Burkholderia xenovorans LB400] (438 aa)
Score = 331, Expect = 4.2e-29, Identities = 95/286 (33%), Positives = 156/286 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +RLD +++  F   SR+  +  IE   V ++GK  +K    V   + I L  + ++ E    TP    +EI+YED  ++++NKP  ++VHP + + S TL N + Y +        G P R GIVHRLDK T GL++VA++L++     +    + ++++YLAL+  ++      +DAPI R     TR  V      K ART F+ ++    + +  T    +L TGRTHQIRVH   I + ++ DP+YG     ++          Q L A++L  IHP T + +    D+P++ +
  S:    77 ERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKP-AKIRQPVPLGATIELVPD-LLPEQLAFTPEPVPLEIIYEDDTLVVINKPAGMVVHPAAGNWSGTLLNGLLYRYGDAAA---GLP-RAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGT-IDAPIGRDPRERTRMAVVTSAAGKPARTHFRRVDSAIWERQPVTAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLGLIHPKTGRTMQWRADVPEDME 367
>gi|47459161|ref|YP_016023.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma mobile 163K] >gi|47458490|gb|AAT27812.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma mobile 163K] (298 aa)
Score = 331, Expect = 4.3e-29, Identities = 93/291 (31%), Positives = 160/291 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           R+D  +++    SR+  +  I+ + V VN  ++ K + K+ E  +I +K++ I E   +      +++IV+E++  LI+NK + ++VHP   ++ +TL N + + F +     NG+ +R GIVHR+DK T GL++VAK+ ++ N F  L    +IE+KY A++   +      ++ PI R  +S  +      ++KEA T    +   +  +L + EL TGRTHQIRVH   I   +  D IYG     K   + Q L AY+L F +    K+ + N+ +PKE +E + K+
  S:    13 RIDKFLANSTDYSRNDIQQLIDEHQVYVNDILVRKASFKIKENDQIEIKKQLIKETNAIAQ--NINLDIVFENEDFLIINKRSGMVVHPAPGNMQDTLVNALLFHFKNNLSNINGE-IRPGIVHRIDKDTSGLLLVAKTNEAHNYFALLLKKHQIERKYQAIIVGKMDHTITNINLPIGRNTSSRLKMEVTAHNSKEAFTKITSLKASETHSLIQCELKTGRTHQIRVHLAHINKPIYGDNIYG----KKVDDFNQRLHAYELSFTYK-DNKQYSFNVPLPKEMQEDLIKF 295
>gi|153810897|ref|ZP_01963565.1| hypothetical protein RUMOBE_01281 [Ruminococcus obeum ATCC 29174] >gi|149833293|gb|EDM88375.1| hypothetical protein RUMOBE_01281 [Ruminococcus obeum ATCC 29174] (304 aa)
Score = 331, Expect = 4.7e-29, Identities = 89/282 (31%), Positives = 148/282 (52%)
  Q:    17 LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           LSRS  +  +++  V+VN +I+ K N K      +IL    +  +T  + P    ++I+YED+++++VNKP D++VHP++  +  TL N +           NG  +R GIVHR+DK T G +++ K         +   +  I+++Y A++  +++     VDAPI R     ++      + KEA T +K + ++   T  E  L TGRTHQIRVH   + + ++ D +YG    P H+      GQ L A  L FIHP T + +     +P+ F + + K  K
  S:    28 LSRSYLQKLLKDGAVSVNTRIV-KANYKTQPGDHVILNIPDL--QTPDIKPENIPLDILYEDQWLMVVNKPKDMVVHPSAGHMEGTLVNAVMAHCGDNLSGING-VMRPGIVHRIDKDTTGALLICKDDMVHRNLAEQLKEHSIKRRYRAIVQGNIKEDEGTVDAPIGRHPIDRKKMAINHKNGKEAVTHYKVLERFGQTTYIECRLETGRTHQIRVHMASLGHPLLGDTVYGSSKNPYHLQ-----GQALHAMILGFIHPVTGEYMEFEAPIPEYFSKLLDKLRK 304
>gi|152977723|ref|YP_001343352.1| 23S rRNA pseudouridine synthase D [Actinobacillus succinogenes 130Z] >gi|150839446|gb|ABR73417.1| pseudouridine synthase, RluA family [Actinobacillus succinogenes 130Z] (324 aa)
Score = 330, Expect = 5.3e-29, Identities = 101/289 (34%), Positives = 155/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK---------HINKTTK--YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  IE NLV VNG I + P TKV    +I ++ E  VEE     P    ++IVYED +IL++NKP + +VHP + +   T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+  +VD P+ R  T  R  ++     K A T ++ +  ++N+T   + L TGRTHQIRVH   I + ++ D  YG +         H ++  +    Q L A  L+  HP +   +     +P +F E I
  S:    17 QRLDQTLAELFPDYSRSRLKTWIEGNLVRVNGNIQNIPRTKVLGGEQIEIRAE--VEEETHYEPENLPLDIVYEDDHILVLNKPKNFVVHPGAGNPRGTVLNALLYHYPQI-----AEVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVAFG-VMTKGGKVDEPMARHPTK-RTAMAVHPMGKPAVTHYRIMEHFRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPRNASEHFSEVLRNFQRQALHAIMLRLEHPISGGLMEWFAPLPDDFAELI 308
>gi|153951567|ref|YP_001397630.1| ribosomal large subunit pseudouridine synthase A [Campylobacter jejuni subsp. doylei 269.97] >gi|152939013|gb|ABS43754.1| ribosomal large subunit pseudouridine synthase, RluA family [Campylobacter jejuni subsp. doylei 269.97] (322 aa)
Score = 330, Expect = 5.4e-29, Identities = 94/285 (32%), Positives = 163/285 (57%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYN-GDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY-----LVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           RLD+ ++ K + SR+     IE + V VN KI  K + K+     I +   K+ +E K       DI+I+YED+ +L++NKP++++VH  S   S   A ++ ++ + K    N G  +R G+VHRLDK T G +++AK+  +    ++   D+ + + YLAL+   L+   + V+  + R  ++  ++++ D +   +K A++ F  + K +N TL   +LFTGRTHQIR H   +  H++ D +YG K        G+Y     L AY L FIHP T++++ +   + ++FK
  S:    11 RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISITSLKLYDEIKPQFEVDFDIDILYEDEDLLVLNKPSNLVVHGAS---SVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINVVKTENLTLMAAKLFTGRTHQIRAHLASLNRHILGDSLYGYK--------GKYDCRIMLHAYFLYFIHPKTKEQIFVKAPLMEDFK 293
>gi|196124530|ref|ZP_03116279.1| putative pseudouridylate synthase [Clostridium difficile ATCC 43255] (300 aa)
Score = 330, Expect = 5.6e-29, Identities = 105/287 (36%), Positives = 163/287 (56%)
  Q:     9 ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID--AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +L    FS+ RS++K K E + V VNG +  KP+ KV     I   E KI EE     P   +++I+Y+D  I++VNKP  ++VHPT      T+AN I Y  D++K     + +++  V+RLD  T GLVIVAK+  + +  +    + K+EKKY+ ++   ++     +D PI R    T   + R ID   + + T +K I + +N T+ EV L TGRTHQIRVH   I + +I D +YG  ++++     Q L AYKL+F  P T++++    D+P++ KE I K
  S:    26 LLAKLNFSV-RSLSKMKREKS-VLVNG-VYKKPSLKVYSGDLI---EVKIYEEKANFEPQDLNLQIIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYIDNQK-----ENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYR---PTEDSIKRIIDEIGQSSVTHYKVIERLENATVLEVSLETGRTHQIRVHMAHIGHGIIGDELYG--YVDEELINRQALHAYKLEFEQPRTKEKLKFKADIPEDMKELISK 298
>gi|15803118|ref|NP_289149.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 EDL933] >gi|12517018|gb|AAG57707.1|AE005490_2 suppressor of ftsH mutation [Escherichia coli O157:H7 EDL933] (326 aa)
Score = 330, Expect = 5.8e-29, Identities = 100/290 (34%), Positives = 155/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +   T  N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTXLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|126698644|ref|YP_001087541.1| putative pseudouridylate synthase [Clostridium difficile 630] >gi|115250081|emb|CAJ67901.1| putative pseudouridylate synthase [Clostridium difficile 630] (300 aa)
Score = 330, Expect = 5.9e-29, Identities = 102/277 (36%), Positives = 159/277 (57%)
  Q:    19 RSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RS++K K E + V VNG +  KP+ KV       L E KI EE     P   +++I+Y+D  I++VNKP  ++VHPT      T+AN I Y  D++K     + +++  V+RLD  T GLVIVAK+  + +  +    + K+EKKY+ ++   ++     +D PI R  E S +R +  D   + + T +K I + +N T+ EV L TGRTHQIRVH   I + +I D +YG  ++++     Q L AYKL+F  P T++++    D+P++ KE I K
  S:    35 RSLSKMKREKS-VLVNG-VYKKPSLKVYSGD---LIEVKIYEEKANFEPQDLNLQIIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYIDNQK-----ENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTEDSIKRII--DERGQSSVTHYKVIERLENATVLEVSLETGRTHQIRVHMAHIGHGIIGDELYG--YVDEELINRQALHAYKLEFEQPRTKEKLKFKADIPEDMKELISK 298
>gi|151570931|gb|EDN36585.1| hypothetical protein FTCG_00787 [Francisella tularensis subsp. novicida GA99-3549] (332 aa)
Score = 329, Expect = 6.7e-29, Identities = 98/284 (34%), Positives = 168/284 (59%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP-----KHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +R+D++++ +F   SR+  +  ++   +TVNG+  +KP   V  DEE EI ++     E I E+         +++I++ED  I++++KP ++IVHP + + + T++N + + + D  K+       R GIVHRLDK T GL++ AKS  +++   +   ++K+ +KYLA++   +  +   ++ PI R + + R +++ +   KEA T +  I  Y  FTL E +L TGRTHQIRVH + IK+ ++ D  Y       + +   T   Q L AYKL FIHP T K V     +P++
  S:    23 KRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRA-TKPKHIVLGDEEVEINIELLPTNEWIAEDI--------NLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLP------RAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGT-INQPIGR-DPTNRTKMAINYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAIKTPTRQALHAYKLSFIHPTTAKMVKFKSKLPED 302
>gi|56964104|ref|YP_175835.1| pseudouridine synthase [Bacillus clausii KSM-K16] >gi|56910347|dbj|BAD64874.1| pseudouridine synthase [Bacillus clausii KSM-K16] (302 aa)
Score = 329, Expect = 6.7e-29, Identities = 94/289 (32%), Positives = 149/289 (51%)
  Q:     5 QRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QR+D ++V      SR+  +  I    V VN K + K N+KV +  ++ L E    +E ++L    +DI  ++VYED  +++VNKP  ++VHP     S TL N +  +F  K +      +R GIVHR+DK T GL++ AK   +          +  E++Y A++H  +      +DAPI R     ++     ++++ A T F     +K ++    EL TGRTHQIRVH  +I + +  DP YGPK        GQ L A  L F HP T + +  +  +P E ++ +
  S:    13 QRIDKVVVDLHGQASRTAVQRWINEGAVLVNEKEV-KTNSKVQQGDKVTLTEPA-AQEVELL---GEDIPLDVVYEDSDVIVVNKPRGLVVHPAPGHESGTLVNAL--LFHCKDLSGINGEIRPGIVHRIDKDTSGLIMAAKHDAAHEHLAAQLKAKTTERRYKAIVHGVIPHAKGTIDAPIGRDPKDRQKMAVTHVNSRPAVTHFSLEETFKQYSYISCELETGRTHQIRVHFNYIGHPLAGDPKYGPKKTLPIN--GQALHAETLGFTHPRTGERLRFSAPLPAEMEKLL 295
>gi|123967748|ref|YP_001008606.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. AS9601] >gi|123197858|gb|ABM69499.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. AS9601] (319 aa)
Score = 329, Expect = 7.4e-29, Identities = 96/288 (33%), Positives = 154/288 (53%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETST-RREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD  LVS +   SR+  +H I + LV VN K   +K   K  +  +I +      E    L P K D+ I++ED++I+++NK + +IVHP     S TL N +  +F  K +      LR GIVHRLDK T G ++VAKS ++     K   ++   ++Y+A++H    +   ++   I R + +  + +V  +   + A T +K   ++ N++L   +L TGRTHQIRVH   I + ++ DP+YG          GQ L A KL  IHP   KE+    ++P +F++ +
  S:    28 RLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPP---EPLIYLKPEKMDLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGL--LFHCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAPNSEEGQIVGNIGRDKLNRLKYKVVEETSGRYACTYWKLEERFGNYSLMSFKLDTGRTHQIRVHCAHINHPIVGDPLYGRCKKLPCKLDGQALHAIKLGLIHPINGKEMIFESELPLDFQKLL 313
>gi|157412550|ref|YP_001483416.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9215] >gi|157387125|gb|ABV49830.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9215] (319 aa)
Score = 329, Expect = 7.6e-29, Identities = 96/288 (33%), Positives = 154/288 (53%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETST-RREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD  LVS +   SR+  +H I + LV VN K   +K   K  +  +I +      E    L P K D+ I++ED++I+++NK + +IVHP     S TL N +  +F  K +      LR GIVHRLDK T G ++VAKS ++     K   ++   ++Y+A++H    +   ++   I R + +  + +V  +   + A T +K   ++ N++L   +L TGRTHQIRVH   I + ++ DP+YG          GQ L A KL  IHP   KE+    ++P +F++ +
  S:    28 RLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPP---EPLIYLKPEKMDLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGL--LFHCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAPNSEEGQIVGNIGRDKLNRLKYKVVEETSGRYACTYWKLEERFGNYSLMSFKLDTGRTHQIRVHCAHINHPIVGDPLYGRCKKLPCKLDGQALHAIKLGLIHPINGKEMIFESELPLDFQKLL 313
>gi|89256088|ref|YP_513450.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. holarctica] >gi|115314564|ref|YP_763287.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica OSU18] >gi|167010773|ref|ZP_02275704.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica FSC200] >gi|169656565|ref|YP_001428170.2| RNA pseudouridine synthase, RluA family protein [Francisella tularensis subsp. holarctica FTNF002-00] >gi|89143919|emb|CAJ79138.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. holarctica LVS] >gi|115129463|gb|ABI82650.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica OSU18] >gi|134253232|gb|EBA52326.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. holarctica 257] >gi|157122045|gb|EDO66185.1| hypothetical protein FTAG_00024 [Francisella tularensis subsp. holarctica FSC022] >gi|164551633|gb|ABU61214.2| RNA pseudouridine synthase, RluA family protein [Francisella tularensis subsp. holarctica FTNF002-00] (332 aa)
Score = 329, Expect = 7.8e-29, Identities = 98/284 (34%), Positives = 167/284 (58%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP-----KHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +R+D+ ++ +F   SR+  +  ++   +TVNG+  +KP   V  DEE EI ++     E I E+         +++I++ED  I++++KP ++IVHP + + + T++N + + + D  K+       R GIVHRLDK T GL++ AKS  +++   +   ++K+ +KYLA++   +  +   ++ PI R + + R +++ +   KEA T +  I  Y  FTL E +L TGRTHQIRVH + IK+ ++ D  Y       + +  T    Q L AYKL FIHP T K V     +P++
  S:    23 KRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRA-TKPKHIVLGDEEVEINIELLPTNEWIAEDI--------NLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLP------RAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGT-INQPIGR-DPTNRTKMAINYRGKEAITYYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIHPTTAKMVKFKSKLPED 302
>gi|189219158|ref|YP_001939799.1| Pseudouridylate synthase, 23S RNA-specific [Methylokorus infernorum V4] >gi|189186016|gb|ACD83201.1| Pseudouridylate synthase, 23S RNA-specific [Methylacidiphilum infernorum V4] (325 aa)
Score = 329, Expect = 8.0e-29, Identities = 95/287 (33%), Positives = 150/287 (52%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           QRLD+ +SS  ++SR+  K KI +  + +    + +P+ ++    EI ++   + EE   L P  ++I  EI+YED+ ILIVNK   ++VHP+    S TL N +  +F   +       LR GIVHRLDK T G++++AK+  S  +    F  + ++K YL L  N         +A I R  +  ++     +  K A T F  +      +  + E  +GRTHQIRVH   +   +I DP+YG K + K   +   L AY LK  HP + K++     +P++FKE
  S:    24 QRLDLFLSSLLNVSRNKIKKKILSGDLRLKNGAVLEPSHRIRGIEEIEIRG-GLTEEIPSL-PKAEEIALEILYEDEEILIVNKQRGMVVHPSCGHWSGTLVNSL--LFHYGESLPGSSLLRPGIVHRLDKDTSGVMVIAKTERSLKSLLLQFSQRTVQKVYLCLCKNRFPYLRYSFEANIHRHASDRKKMAVHRLKGKTAETRFTLLFASSQASFLKCEPVSGRTHQIRVHLSHLGFPIIGDPLYG-KGVRK-YPFPLLLHAYALKIEHPRSGKKIEFMAPLPQDFKE 306
>gi|119897309|ref|YP_932522.1| pseudouridylate synthase [Azoarcus sp. BH72] >gi|119669722|emb|CAL93635.1| pseudouridylate synthase [Azoarcus sp. BH72] (324 aa)
Score = 328, Expect = 8.6e-29, Identities = 89/292 (30%), Positives = 155/292 (53%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           RLD +++  F   SRS  +  +++ L+ ++G +  +   KV    E+++     + E     P    +++VYED  IL+++KP  ++VHP S + S TL N + +          G P R GIVHRLDK T GL++VAK+L++     +    + + + Y AL++  + +   E+DA I R     R  ++     + A T +    +    TL E  L TGRTHQIRVH   + + ++ DP+YGP+ +  +   G   Q L A++L  +HP + +++  +  +P +F   ++K G
  S:    32 RLDQVLARLFPEHSRSRLQAWLKDGLIRLDG-MERQAKHKVHGGEELVVAGLPPLPEQLAFEPEAIPLDVVYEDASILVIDKPAGLVVHPGSGNWSGTLLNALLH----HAPALAGLP-RAGIVHRLDKDTTGLMVVAKTLEAQTDLVRQLQQRTVARHYYALVYGDIASDG-EIDADIDR-HPVQRTRMAVVPGGRPALTRYAVRQRLHGLTLVECRLQTGRTHQIRVHMAHLGHPLVGDPVYGPRRVTDSRVDGFSRQALHAFRLGLLHPASGEDMVWSAPLPADFAALLEKVG 319
>gi|194435119|ref|ZP_03067355.1| ribosomal large subunit pseudouridine synthase D [Shigella dysenteriae 1012] >gi|194416650|gb|EDX32783.1| ribosomal large subunit pseudouridine synthase D [Shigella dysenteriae 1012] (326 aa)
Score = 328, Expect = 9.4e-29, Identities = 99/290 (34%), Positives = 155/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++      + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHMRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|157164896|ref|YP_001467348.1| P-protein [Campylobacter concisus 13826] >gi|112801995|gb|EAT99339.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Campylobacter concisus 13826] (323 aa)
Score = 328, Expect = 9.5e-29, Identities = 102/293 (34%), Positives = 165/293 (56%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILK---EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKI--KYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLV-AYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           N+ RLD++V+ +  +SR+ A + I+++LV+VN K +SKP+  + E  EI +    ++++  E +V      DI I+YED  ++++NKP  I+VH      S   A +++++     +    NGD +R GIVHRLDK T G ++VAK+  +    ++   D+ + + YLAL    L+   + +D PI R   + R + +   DAK A++ F  +       L   +LFTGRTHQIRVH   I  H++ D +YG K  ++  K  + ++ AY L FIHP T K V        +F + I K
  S:     8 NSSRLDVVVAKELQISRNQALNLIKDSLVSVNLKPVSKPSFLLSENDEICVNFAPKKEVQNEYEV----NFDIPIIYEDDDLIVLNKPPQIVVHQAP---SVKEATLVEWLNKKGFMLSNLNGD-VRAGIVHRLDKGTSGAIVVAKNNFAHAKLSEQLSDKSMGRIYLALTDLPLKEDII-IDKPIGR-NPNNRLKKAIVADAKFAKSAFVNLLSEGGVNLIAAKLFTGRTHQIRVHLASINRHILGDDLYGFK--SQGDKISRVMLHAYMLYFIHPRTGKRVEFTAKTYDDFNQIIYK 294
>gi|83589720|ref|YP_429729.1| ribosomal large subunit pseudouridine synthase D [Moorella thermoacetica ATCC 39073] >gi|83572634|gb|ABC19186.1| ribosomal large subunit pseudouridine synthase D [Moorella thermoacetica ATCC 39073] (306 aa)
Score = 328, Expect = 9.5e-29, Identities = 92/291 (31%), Positives = 147/291 (50%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVN--GKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  ++ +   +SRS  +  +E   +T+   G++ +    +  E   + L E  ++       P    ++I+YED+ I++VNKP  ++VHP       TL N + Y   D   I  NG  LR GIVHRLDK T G+++ AK+  +         D  +++ YLAL+H  +      V+API R     +R      +++ A T ++ +  +  +TL E  L TGRTHQIRVH  FI + V+ DP YGP+        GQ L A  L F+HP     +      P  F + +++
  S:    12 RRIDAWLAGELPEVSRSRIQQLLEAGEITLALPGRLKANYRLRGGERVRVRLPEPTLLAARPEAIP----LDILYEDEDIIVVNKPQGMVVHPAPGSEGGTLVNALLYHCGDLSGI--NG-VLRPGIVHRLDKDTSGILVAAKNDAAHRGLAAQIKDHSMKRIYLALVHGEVAEPRGRVEAPIGRHPVDRQRMAVTLKNSRPAVTHYRVVEHFPGYTLLEARLETGRTHQIRVHMAFIGHPVVGDPKYGPRRCPFAVP-GQLLHAGCLGFVHPVRGDYLEFTTPPPSIFLQVLEQ 298
>gi|168715037|ref|ZP_02747314.1| putative pseudouridylate synthase [Clostridium difficile QCD-63q42] (300 aa)
Score = 328, Expect = 9.6e-29, Identities = 102/277 (36%), Positives = 159/277 (57%)
  Q:    19 RSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RS++K K E + V VNG +  KP+ KV       L E KI EE     P   +++I+Y+D  I++VNKP  ++VHPT      T+AN I Y  D++K     + +++  V+RLD  T GLVIVAK+  + +  +    + K+EKKY+ ++   ++     +D PI R  E S +R +  D   + + T +K I + +N T+ EV L TGRTHQIRVH   I + +I D +YG  ++++     Q L AYKL+F  P T++++    D+P++ KE I K
  S:    35 RSLSKMKREKS-VLVNG-VYKKPSLKVYSGD---LIEVKIDEEKANFEPQDLNLQIIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYIDNQK-----ENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTEDSIKRII--DERGQSSVTHYKVIERLENATVLEVSLETGRTHQIRVHMAHIGHGIIGDELYG--YVDEELINRQALHAYKLEFEQPRTKEKLKFKADIPEDMKELISK 298
>gi|134095125|ref|YP_001100200.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA) [Herminiimonas arsenicoxydans] >gi|133739028|emb|CAL62076.1| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) [Herminiimonas arsenicoxydans] (318 aa)
Score = 328, Expect = 1.0e-28, Identities = 95/292 (32%), Positives = 155/292 (53%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINK----YKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           RLD ++S+     SRS  +  I+   V+V+G+I     T   +E  +I  +     E +   P   D+ I YED  IL+++KP  ++VHP + + S TL N + +   +      G P R GIVHRLDK T GL++VAK+L +     +    + ++++YLAL+       + +VD  I R      +  VS ++ AK A T F+ +       +  +L   +L TGRTHQIRVH + I   ++ D +YG +H+  T    Q L A +L  +HP +   V  + ++P++F + I + G
  S:    26 RLDKVLSTLVPQYSRSRLQQWIDAGHVSVDGEIARAKMTVYGDEKVVIYPQP--APEDEAFKPEAMDLNIAYEDAAILVIDKPAGLVVHPAAGNWSGTLLNGLLHYLPA----IAGVP-RAGIVHRLDKDTSGLMVVAKTLVAHTDLVRQLQARTVKREYLALVWGTPNV-SGKVDTSIGRHSRDRVKMAVSENLTAKPALTHFQRLATGMLDGRPVSLMMCQLETGRTHQIRVHMQSIGFALVGDALYGKQHLT-TVFPRQALHARRLGLVHPVSGAAVEWSSELPQDFADLIARSG 314
>gi|187923831|ref|YP_001895473.1| pseudouridine synthase, RluA family [Burkholderia phytofirmans PsJN] >gi|187715025|gb|ACD16249.1| pseudouridine synthase, RluA family [Burkholderia phytofirmans PsJN] (431 aa)
Score = 328, Expect = 1.0e-28, Identities = 95/286 (33%), Positives = 154/286 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +RLD +++  F   SR+  +  IE   V ++GK  +K    V   + I L  + ++ E    TP    +EIVYED  ++++NKP  ++VHP + + S T+ N + Y +        G P R GIVHRLDK T GL++VA++L++     +    + ++++YLAL+  ++      +DAPI R     TR  V      K ART F+ ++    + +  T    +L TGRTHQIRVH   I + ++ DP+YG     ++          Q L A++L  IHP T + +    D P + +
  S:    77 ERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKP-AKIRQPVPLGATIELVPD-LLPEQLAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA---GLP-RAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGT-IDAPIGRDPRERTRMAVVTSASGKPARTHFRRVDSAIWQRQPVTAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGLIHPQTGRTMQWRADAPADME 367
>gi|116626305|ref|YP_828461.1| ribosomal large subunit pseudouridine synthase D [Solibacter usitatus Ellin6076] >gi|116229467|gb|ABJ88176.1| ribosomal large subunit pseudouridine synthase D [Solibacter usitatus Ellin6076] (296 aa)
Score = 327, Expect = 1.1e-28, Identities = 88/289 (30%), Positives = 155/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNT-KVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QR+D  + +     SRS  +  I++  V VNG  +    T +  +  E+   +   +  T    P    + I+YED  ++ ++KP  ++VH  +   S TL N + + F +  +   G PLR GIVHRLD+ T G+++VAK+  +       F  ++IEK YLAL+H  ++  T  ++ PI R      R  +R  + + A + ++ + ++ +FTL EV + TGRTHQIRVH   I++ V+ D +YG        +Y  +L A++++F  P + +E+ I   +P + + ++
  S:    12 QRIDQWLHAHLPDFSRSRIQEWIKSARVRVNGAAVKTSYTLRAADAVEVEPADPPPLNATAEDIP----LRILYEDADVVAIDKPAGMVVHAGAGVHSGTLVNALLHRFAT--LSGVGGPLRPGIVHRLDRFTSGVLLVAKNDAAHQKLAAQFSGREIEKVYLALVHGTVKPETGRIERPIARDPVHRARMTARLAEGRAAWSEYRVLRRFPDFTLLEVRIGTGRTHQIRVHLASIRHPVVGDTLYGAPAQPLLGRY--FLHAHRIRFHLP-SGREMLIESPLPPDLEAWL 293
>gi|170692348|ref|ZP_02883511.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M] >gi|170142778|gb|EDT10943.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M] (450 aa)
Score = 327, Expect = 1.1e-28, Identities = 95/284 (33%), Positives = 154/284 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +RLD +++  F   SR+  +  IE   V ++GK  +K    V   + I L  + ++ E    TP    +EIVYED  ++++NKP  ++VHP + + S T+ N + Y +        G P R GIVHRLDK T GL++VA++L++     +    + ++++YLAL+  ++      +DAPI R     TR  V      K ART F+ ++    + +  T    +L TGRTHQIRVH   I + ++ DP+YG     ++          Q L A++L  IHP T + +    D+P +
  S:    77 ERLDKVLARLFPEFSRNRLQSWIEAERVRIDGKP-AKIRQPVPLGATIELVPD-LLPEQLAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA---GLP-RAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGT-IDAPIGRDPRERTRMAVVTGASGKPARTHFRRVDTAIWQRQPVTAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGEFARQALHAWRLGLIHPKTGRTMQWRADVPAD 365
>gi|170766082|ref|ZP_02900893.1| ribosomal large subunit pseudouridine synthase D [Escherichia albertii TW07627] >gi|170125228|gb|EDS94159.1| ribosomal large subunit pseudouridine synthase D [Escherichia albertii TW07627] (326 aa)
Score = 327, Expect = 1.1e-28, Identities = 99/290 (34%), Positives = 156/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E ++
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIV-----DVPRAGIVHRLDKDTTGLMVVAKNVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELVE 310
>gi|11279841|pir||A81748 ribosomal large chain pseudouridine synthase D TC0029 [imported] - Chlamydia muridarum (strain Nigg) (345 aa)
Score = 327, Expect = 1.2e-28, Identities = 98/290 (33%), Positives = 163/290 (56%)
  Q:     6 RLDI-LVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEET-KVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHN-----HLQTRTVEVDAPIKRVETSTRREVSRDID-AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  LV    + SR+  + +I+   V VNG++ ++ +  + +   + L  E + EET   LTP    ++ VYED  IL++NKP +++VHP    +  T+ + ++  I +  K ++  +P R GIVHRLDK T GL+I  K+  +   +++LF  ++++K Y+A+  N     H+ TR      P+KR E +    +S+D +  KEA T    +      ++  +   TGRTHQ+RVH + +   ++ DP+YG   IN   +YG   Q L AY L F HP + + V +   +P +    I+K
  S:    33 RLDKGLVLHNNAYSRAFYQQQIDLGRVRVNGRVQTRASYLLSQGDLVDL--ELVEEETPSSLTPENIPLDKVYEDNMILVINKPRNMVVHPAPGHVQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKAVYSELFSSKQMKKMYIAICINSPAQKHIHTRIAR--HPVKRKEMTV---LSKDTEGGKEAITHCHVLASNGRLSVVALYPETGRTHQLRVHMKHLGTPILGDPVYGVPSIN--FRYGLDKQQLHAYSLVFTHPESAERVELVTKLPDDMTSLIEK 325
>gi|62260278|gb|AAX77894.1| unknown protein [synthetic construct] (367 aa)
Score = 327, Expect = 1.2e-28, Identities = 98/284 (34%), Positives = 167/284 (58%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP-----KHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +R+D+ ++ +F   SR+  +  ++   +TVNG+  +KP   V  DEE EI ++     E I E+         +++I++ED  I++++KP ++IVHP + + + T++N + + + D  K+       R GIVHRLDK T GL++ AKS  +++   +   ++K+ +KYLA++   +  +   ++ PI R + + R +++ +   KEA T +  I  Y  FTL E +L TGRTHQIRVH + IK+ ++ D  Y       + +  T    Q L AYKL FIHP T K V     +P++
  S:    49 KRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRA-TKPKHIVLGDEEVEINIELLPTNEWIAEDI--------NLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLP------RAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGT-INQPIGR-DPTNRTKMAINYRGKEAITHYTSIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIHPTTAKMVKFKSKLPED 328
>gi|56708307|ref|YP_170203.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. tularensis SCHU S4] >gi|110670778|ref|YP_667335.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. tularensis FSC198] >gi|54113047|gb|AAV29157.1| NT02FT0135 [synthetic construct] >gi|56604799|emb|CAG45878.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. tularensis SCHU S4] >gi|110321111|emb|CAL09261.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. tularensis FSC 198] >gi|151569033|gb|EDN34687.1| hypothetical protein FTBG_00600 [Francisella tularensis subsp. tularensis FSC033] (332 aa)
Score = 327, Expect = 1.3e-28, Identities = 98/284 (34%), Positives = 167/284 (58%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP-----KHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +R+D+ ++ +F   SR+  +  ++   +TVNG+  +KP   V  DEE EI ++     E I E+         +++I++ED  I++++KP ++IVHP + + + T++N + + + D  K+       R GIVHRLDK T GL++ AKS  +++   +   ++K+ +KYLA++   +  +   ++ PI R + + R +++ +   KEA T +  I  Y  FTL E +L TGRTHQIRVH + IK+ ++ D  Y       + +  T    Q L AYKL FIHP T K V     +P++
  S:    23 KRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRA-TKPKHIVLGDEEVEINIELLPTNEWIAEDI--------NLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLP------RAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGT-INQPIGR-DPTNRTKMAINYRGKEAITHYTSIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIHPTTAKMVKFKSKLPED 302
>gi|145954769|ref|ZP_01803773.1| hypothetical protein CdifQ_04001164 [Clostridium difficile QCD-32g58] >gi|168693828|ref|ZP_02726105.1| putative pseudouridylate synthase [Clostridium difficile QCD-37x79] >gi|168724141|ref|ZP_02756418.1| putative pseudouridylate synthase [Clostridium difficile QCD-76w55] >gi|168732269|ref|ZP_02764546.1| putative pseudouridylate synthase [Clostridium difficile QCD-97b34] >gi|196162141|ref|ZP_03122702.1| putative pseudouridylate synthase [Clostridium difficile CIP 107932] (300 aa)
Score = 327, Expect = 1.3e-28, Identities = 102/277 (36%), Positives = 159/277 (57%)
  Q:    19 RSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RS++K K E + V VNG +  KP+ KV       L E KI EE     P   +++I+Y+D  I++VNKP  ++VHPT      T+AN I Y  D++K     + +++  V+RLD  T GLVIVAK+  + +  +    + K+EKKY+ ++   ++     +D PI R  E S +R +  D   + + T +K I + +N T+ EV L TGRTHQIRVH   I + +I D +YG  ++++     Q L AYKL+F  P T++++    D+P++ KE I K
  S:    35 RSLSKMKKEKS-VLVNG-VYKKPSLKVYSGD---LIEVKIDEEKANFEPQDLNLQIIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYIDNQK-----ENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTEDSIKRII--DERGQSSVTHYKVIERLENATVLEVSLETGRTHQIRVHMAHIGHGIIGDELYG--YVDEELINRQALHAYKLEFEQPRTKEKLKFKADIPEDMKELISK 298
>gi|168186171|ref|ZP_02620806.1| ribosomal large subunit pseudouridine synthase D [Clostridium botulinum C str. Eklund] >gi|169295643|gb|EDS77776.1| ribosomal large subunit pseudouridine synthase D [Clostridium botulinum C str. Eklund] (304 aa)
Score = 327, Expect = 1.4e-28, Identities = 99/293 (33%), Positives = 164/293 (55%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIE-NNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           RLD+ +S  F   SRS A+  IE  N+   N    S    K+ +  EI +KE++ +     + P    + I+YED+ +++++KP  ++VHP + + S TL N + Y  DS     NGD +R GIVHR+DK T G+++VAK+  +    ++   +  ++++Y+AL+   ++     +DAP+ R  +   +R V R+   K A T +  + ++   TL +  L TGRTHQIRVH   I + ++ DP+YG +   +    GQ L A KL FIHP ++K +    ++P  +KE + K  K
  S:    16 RLDVFISKCFEEKSRSYAQKLIEEKNVFVNNSSKKSNYKLKIGDYVEIKIKEDEKIN----IKPEDIKLNIIYEDEDVIVIDKPQGMVVHPGAGNYSGTLVNGLLYHCDSLS-SINGD-VRPGIVHRIDKDTSGVLVVAKNDSAHIILSEQLKEHSMKREYIALVEGIIKNDEGIIDAPLGRNPKDRIKRAVVRN--GKSAVTHYNVLRRFNKNTLVKCILETGRTHQIRVHMAHINHPLVGDPMYGFRK-QRFKLNGQMLHARKLGFIHPSSKKYMEFQSELPNYYKEILFKLSK 302
>gi|134301739|ref|YP_001121707.1| pseudouridine synthase, RluA family protein [Francisella tularensis subsp. tularensis WY96-3418] >gi|134049516|gb|ABO46587.1| pseudouridine synthase, RluA family protein [Francisella tularensis subsp. tularensis WY96-3418] (317 aa)
Score = 327, Expect = 1.4e-28, Identities = 98/284 (34%), Positives = 167/284 (58%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP-----KHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +R+D+ ++ +F   SR+  +  ++   +TVNG+  +KP   V  DEE EI ++     E I E+         +++I++ED  I++++KP ++IVHP + + + T++N + + + D  K+       R GIVHRLDK T GL++ AKS  +++   +   ++K+ +KYLA++   +  +   ++ PI R + + R +++ +   KEA T +  I  Y  FTL E +L TGRTHQIRVH + IK+ ++ D  Y       + +  T    Q L AYKL FIHP T K V     +P++
  S:     8 KRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRA-TKPKHIVLGDEEVEINIELLPTNEWIAEDI--------NLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNTLLHRYKDQDKLP------RAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGT-INQPIGR-DPTNRTKMAINYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIHPTTAKMVKFKSKLPED 287
>gi|123965457|ref|YP_001010538.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9515] >gi|123199823|gb|ABM71431.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9515] (320 aa)
Score = 327, Expect = 1.4e-28, Identities = 95/289 (32%), Positives = 152/289 (52%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDA-KEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD  LVS +   SR+  ++ I   LV +N K   +K   K  +  +I +      E    L P K  + I+YED++I+++NK + +IVHP     S TL N +  +F  K +      LR GIVHRLDK T G ++VAKS +S         D+   + Y+A++H    T   ++   I R + +  +    D ++ + A T +K + ++ N++L   +L TGRTHQIRVH  +I + ++ DP+YG          GQ L A +L   HP   +E+    D+P+EF + ++
  S:    28 RLDRWLVSKRPEQSRARIQNLINAGLVLINYKTAKAKTPLKTGDNIQIWMPPP---EPLVYLKPEKMHLNILYEDEHIIVINKQSGLIVHPAPGHKSGTLVNGL--LFHCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQESLVNLQIQIRDKIASRNYIAVIHGVPNTSEGKIVGHIGRDKINRLKYAVVDENSGRYACTYWKLLERFGNYSLMSFKLDTGRTHQIRVHCAYINHPILGDPLYGRCKKLPCKLDGQALHAIELGLFHPINGEEMKFEADLPQEFVKLLR 314
>gi|189502073|ref|YP_001957790.1| hypothetical protein Aasi_0665 [Candidatus Amoebophilus asiaticus 5a2] >gi|189497514|gb|ACE06061.1| hypothetical protein Aasi_0665 [Candidatus Amoebophilus asiaticus 5a2] (341 aa)
Score = 326, Expect = 1.4e-28, Identities = 96/281 (34%), Positives = 154/281 (54%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           SR+  +  I+N  + VNG I +K N K+   ++ +I+L       E   L P    ++IVYED+ +++V+KP  ++VHP   + + TL N + Y FD+     N +  R G+VHR+DK T GL++VAK+  S  A  K F D  I + Y AL+    +T T  +D  + R     RR V+   +    K A T ++ + + +  +L +  L TGRTHQIR H + + + +  D  YG   I K  ++ +Y               L AY L FIHP TQ+ +     +P +F+  + ++ K
  S:    42 SRNKIQLAIDNQFILVNG-IPTKANYKIRPYDKIQIVLPNPPRNNE---LIPENIPLDIVYEDEALMVVHKPAGMVVHPGYNNWTGTLVNALIYYFDNLPTAPN-NIGRPGLVHRIDKDTSGLLVVAKTEASLIALAKQFYDHSIARTYYALIWGEPETETGTIDINLDR-SLQDRRIVAPYTNPEKGKRAVTHYQVVERLRYVSLVKCTLETGRTHQIRAHMKHMGHPIFADAAYGGHEIVKGEQFSKYKSFVENCFQIMPRQALHAYSLGFIHPTTQENMYFESPLPTDFQTVLNRWSK 336
>gi|57238152|ref|YP_179402.1| ribosomal large subunit pseudouridine synthase D [Campylobacter jejuni RM1221] >gi|57166956|gb|AAW35735.1| ribosomal large subunit pseudouridine synthases, RluD subfamily [Campylobacter jejuni RM1221] (322 aa)
Score = 326, Expect = 1.5e-28, Identities = 91/285 (31%), Positives = 159/285 (55%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYN-GDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           RLD+ ++ K + SR+     IE + V VN KI  K + K+     I +   K+  E K       DI+++YED+ +L++NKP++++VH  S   S   A ++ ++ + K    N G  +R G+VHRLDK T G +++AK+  +    ++   D+ + + YLAL+   L+   + V+  + R  ++  ++++ D +   +K A++ F  + K +N TL   +LFTGRTHQIR H   +  H++ D +YG    N        L AY L FIHP T++++ +   + ++FK
  S:    11 RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISIASLKLCNEIKPQFEVDFDIDVLYEDEDLLVLNKPSNLVVHGAS---SVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGSILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINVVKTENLTLMAAKLFTGRTHQIRAHLASLNRHILGDGLYG---YNGKYDCRIMLHAYFLYFIHPKTKEQIFVKAPLMEDFK 293
>gi|153953824|ref|YP_001394589.1| pseudouridine synthase [Clostridium kluyveri DSM 555] >gi|146346705|gb|EDK33241.1| Predicted pseudouridine synthase [Clostridium kluyveri DSM 555] (305 aa)
Score = 326, Expect = 1.5e-28, Identities = 102/288 (35%), Positives = 155/288 (53%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD+ +       SRS  ++ IE+NLV VN ++  K N K      I +     VE    L    +DI  +I+YED  +++VNKP  +IVHP S   + TL N +           NG   R GIVHR+DK T G++++AK+  S N  ++   D  + ++Y+AL+   ++     +D PI R     + +++     K A T ++ I ++K +TL +  L TGRTHQIRVH  ++ + V+ DP+YG K   K    GQ L A KL FIHP T   +   +++P+ FK  I
  S:    16 RLDLFICKHIQDKSRSYIQNLIEDNLVEVNHRM-KKSNYKTKTGDNIKVSLPDAVE----LNIKGEDIKLDILYEDSDVIVVNKPQGMIVHPASGVYTGTLVNALLNHCREDLSGINGIA-RPGIVHRIDKDTSGILVIAKNDMSHNKLSEQLKDHSMTREYIALVEGIIKEEKGSLDKPIGR-HKKDKIKMAVVEGGKRAVTHYEVIKRFKEYTLVKCILETGRTHQIRVHMCYLGHPVVGDPVYGYKK-QKFNLKGQLLHAQKLGFIHPGTGTYMEFQVEVPEYFKRII 298
>gi|166031852|ref|ZP_02234681.1| hypothetical protein DORFOR_01553 [Dorea formicigenerans ATCC 27755] >gi|166028305|gb|EDR47062.1| hypothetical protein DORFOR_01553 [Dorea formicigenerans ATCC 27755] (302 aa)
Score = 326, Expect = 1.6e-28, Identities = 88/278 (31%), Positives = 148/278 (53%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           SRS  +  I+   + VN K + K N ++   +  E+ + E K  +    + P    ++I+YED+ +++VNKP  ++VHP     S TL N + Y   ++    NG   R GIVHR+D  T G +I+ K+  +  +      +  I + Y A++H +++     V+API R  T  ++      +A+ A T +K + ++ ++T  + +L TGRTHQIRVH   I + ++ D +YGPK    +   GQ L A  L FIHP T + + +N  +P  F   ++K
  S:    27 SRSYLQKLIKEQYIKVNNKPV-KANYRLVLGDRVEVCIPEAKEPD----IEPENIPLDILYEDEDVIVVNKPKQMVVHPAPGHYSGTLVNALMYHCGNELSGINGTS-RPGIVHRIDMDTTGSLIICKNDMAHQSLAVQLEEHSINRIYEAIVHGNIKEEEGTVNAPIGRHPTDRKKMSIHAKNARNAITHYKVLKRFGDYTYIQCKLETGRTHQIRVHMASIGHPLLGDQVYGPKKCPFSKLVGQTLHARTLGFIHPRTNEYIEVNAPLPDYFLNLLEK 300
>gi|188996123|ref|YP_001930374.1| pseudouridine synthase, RluA family [Sulfurihydrogenibium sp. YO3AOP1] >gi|188931190|gb|ACD65820.1| pseudouridine synthase, RluA family [Sulfurihydrogenibium sp. YO3AOP1] (318 aa)
Score = 326, Expect = 1.6e-28, Identities = 104/296 (35%), Positives = 164/296 (55%)
  Q:     3 NTQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYK--NFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQ---------YLVAYKLKFIHPFTQKEVNINL-DMPKEFKEYIKKYGK 298
           + +RLD  ++  +   SRS  ++ IEN  V ++   + K +TKV    E  +                  +EI YED+ + +V KP  ++VHP+    S TL N + Y F +   +Y G   R GIVHRLDK T GL+IVAKS  +     K+F D++I+KKY A++   ++     +D PI R   + ++  +   + K+A T +    +++  N TL +++L TGRTHQIRVH   I + + ND +YG K  N ++   +          LVAYKL F HP T + ++I L  +PKE +E +++  K
  S:    14 SNKRLDQFLALVYPEYSRSFYQNLIENRFVLLDNNPVRKSSTKVKTGQEFTIIIPPPEPLEIEPE--NIPLEIYYEDEDLAVVYKPPGMVVHPSVGHTSGTLVNALLYHFKNVS-QYQGKE-RAGIVHRLDKDTAGLLIVAKSEFAHKELQKMFQDREIDKKYKAIVSGIVKKDHGLIDLPIGRSIYNRQKMGTVATNPKDALTEYWVEKRFEKHNLTLVDIKLHTGRTHQIRVHFSAIGHPLFNDFVYGFKKSNLSSDLAKNLSDKLKYHALVAYKLTFRHPRTNQMLSIELKSLPKEIEEILQELSK 318
>gi|157363878|ref|YP_001470645.1| RluA family pseudouridine synthase [Thermotoga lettingae TMO] >gi|157314482|gb|ABV33581.1| pseudouridine synthase, RluA family [Thermotoga lettingae TMO] (298 aa)
Score = 326, Expect = 1.7e-28, Identities = 97/289 (33%), Positives = 157/289 (54%)
  Q:     6 RLDILVSSKF--SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD+ +  +   ++SRS  +  I+   VTVN  +I KPN +V +  +++        ++  + P    I ++YED+ I++VNKP  +IVHP     S TL N +  ++  K +K  G  LR GIVHRLDK T G+++VAK+  + +  +  F D+K+ K YLAL+   ++    ++   I R      +  + +I  + A T +K I  +++ TL      TGRTHQIRVH + I + ++ D +YG      +    Q L A KL F HP T + +     +P++FKE I+
  S:    11 RLDLFLLQRIPKAISRSFVQRAIKEGKVTVN-DVIRKPNYRV-KFGDVVKISIPSNAQSISIEPEPIQIGVIYEDEDIIVVNKPAGMIVHPIPSHNSGTLVNAL--LYHCKDLKGIGGELRPGIVHRLDKDTSGVMVVAKNDFAHHNLSNQFKDRKVFKMYLALVSGKVEHLEGDIQISIARHPVLRTKMAASEI-GRIAVTHYKVIKYFEHATLLMAFPKTGRTHQIRVHMKCINHPILGDKLYG----KGSGASRQMLHATKLGFYHPRTHEWIEFIAPLPEDFKETIR 292
>gi|163724669|ref|ZP_02132198.1| pseudouridine synthase, RluA family [Desulfatibacillum alkenivorans AK-01] >gi|161402173|gb|EDQ26412.1| pseudouridine synthase, RluA family [Desulfatibacillum alkenivorans AK-01] (321 aa)
Score = 325, Expect = 1.8e-28, Identities = 96/290 (33%), Positives = 155/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPN--TKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRR-EVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--------PKHI--NKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  V     +LSR+     I   LVTV+ K + KP+   K  E   + + E     ET  +     D+ I+YED+ I+ VNKP  ++VHP     SNTL N +  +   K +   G   R GIVHRLDK T G+++ AK+  +    ++    +++EK YLAL H  ++  T  +D P+ R  +  +R  VS     +EA +++    ++ + T  +V++ TGRTHQIRVH   + + VI D +YG        P  +         Q L A+ + F HP T +++ +   +P++  + ++
  S:    18 QRLDAFVPVHCKNLSRNACARLIRQGLVTVD-KSVKKPSYVLKPGEMVSVTVPEP----ETADIVAQDMDLAILYEDRDIVAVNKPPGMVVHPAPGHSSNTLVNAL--LAHCKDLSGIGGVQRPGIVHRLDKETSGVILAAKNDAAHAGLSEQLAQRRVEKFYLALAHGVIKEDTGVIDLPLARHPSDRKRMHVSTPAKGREALSLWTVKERFLDATYVKVQIKTGRTHQIRVHLAALHHPVIGDTVYGGRKKRGRLPASVLGKAPPPERQMLHAHIVSFTHPVTGEKLTLTAPLPQDMAQLLE 314
>gi|88856520|ref|ZP_01131177.1| ribosomal large subunit pseudouridine synthase [marine actinobacterium PHSC20C1] >gi|88814174|gb|EAR24039.1| ribosomal large subunit pseudouridine synthase [marine actinobacterium PHSC20C1] (301 aa)
Score = 325, Expect = 1.8e-28, Identities = 87/286 (30%), Positives = 150/286 (52%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKD-IEIVYEDKYILIVNKPNDIIVHPT-SYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           QR+D  ++     SR+ A    E   VT+NG ++ K +      +E  L+   + +    + P   D + IVY+D++I++++KP  +  HP+  +D    L  +    +   +I  +G   R GIVHRLD  T GL++VAKS  ++    + F D+++ K Y +++  H       +DAPI R   S+ +  +     K++ T ++ +  + + +L EV+L TGRTHQIRVH    ++  + D +YG  P    K     Q+L A+KL F+HP T++ V      P + +
  S:    10 QRVDAALAKLLGFSRTFAAEVAEEGGVTMNGVVVGKSDRL---SAEAWLEVSWVSKSEPQIVPVVLDTLGIVYDDEHIVVIDKPAGVAAHPSIGWDGVTVLGALAGAGY---RISTSGAAERAGIVHRLDAGTSGLMVVAKSELAYTELKRAFHDREVNKIYHSIVQGHPDPLMGTIDAPIGRHPGSSWK-FAVVAGGKDSITHYETLEAFPSASLVEVQLETGRTHQIRVHMAAQRHPCVGDTMYGADPTISAKLGLTRQWLHAHKLGFVHPATREPVTFESPYPADLQ 292
>gi|15606824|ref|NP_214204.1| hypothetical protein aq_1758 [Aquifex aeolicus VF5] >gi|3915479|sp|O67638|Y1758_AQUAE Uncharacterized RNA pseudouridine synthase aq_1758 (RNA-uridine isomerase) (RNA pseudouridylate synthase) >gi|2984062|gb|AAC07603.1| hypothetical protein aq_1758 [Aquifex aeolicus VF5] (316 aa)
Score = 325, Expect = 1.9e-28, Identities = 98/286 (34%), Positives = 153/286 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNF--TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG------PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +RLD  ++  +   SRS  K  ++  LV VNG+ + KP+ K+ E   +IL   +   E   + P    I I+YED+ I +V KP  ++VHP+    S TL N +  ++  K +   G   R GIVHRLDK T G++++AK+  +     + F ++K EK Y  L+   ++     +D PI R     +R   R  + KEA T +  + +Y+ +  TL +V++ TGRTHQIRVH   I + V+ D  YG      PK +         L+AY L F HP   + +   ++ P+ FK
  S:    16 ERLDKFLARAYPDFSRSYIKKLVKEGLVYVNGEEVRKPSRKLREGERVILHVPE--PEPLDVKPENIPINIIYEDEDIAVVEKPCGLVVHPSPGYTSGTLVNAL--LYHIKDLSSIGGVERPGIVHRLDKETAGVMVIAKNNTAHRNLVRQFQERKTEKFYKVLVKGLVKKDYGAIDTPIARHPVDRKRFWVRK-EGKEALTEYWVLKRYEKYEITLLKVKIHTGRTHQIRVHFASIGHPVLGDRTYGFKSSSVPKELLSLMGECNMLIAYHLGFYHPTKGEWMVFEIEEPETFK 305
>gi|196228386|ref|ZP_03127253.1| pseudouridine synthase, RluA family [Chthoniobacter flavus Ellin428] >gi|196227789|gb|EDY22292.1| pseudouridine synthase, RluA family [Chthoniobacter flavus Ellin428] (302 aa)
Score = 325, Expect = 1.9e-28, Identities = 89/286 (31%), Positives = 152/286 (53%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKE------EKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID-AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           RLD  L S+   LSR+  +  I+   VT+NG + +K + ++     + L E      E + EE          +++++ED  ++++NKP  ++VHP + + S T+ N +  +   + +   G   R GIVHRLDK T G ++VAK+  +  +  K F  +++ K YLAL       ++  ++API R     ++      D  + A+T ++ + +    TL E  L TGRTHQIRVH + + + ++ D +YG     +     Q L A++L F+HP T K +N    +P +F E
  S:    16 RLDQFLASAAAGLSRARIQDLIKEGHVTLNGGV-AKASARLRAGDAVTLHEPPPVPTETVAEEIA--------LDVLFEDDDLIVINKPAGLVVHPAAGNWSGTVVNAL--LHHCQTLSGIGGEQRPGIVHRLDKDTSGCLVVAKNDAAHQSLAKQFAGREVTKIYLALAAGKWARKSGVIEAPIGRHPVQRKKMTVLPADKGRAAKTGYRVLLELPVGTLVECTLHTGRTHQIRVHLKHLGHPILGDEVYG----RRGDFARQMLHAWRLGFVHPGTGKHLNFESPIPPDFVE 294
>gi|82778018|ref|YP_404367.1| 23S rRNA pseudouridine synthase D [Shigella dysenteriae Sd197] >gi|81242166|gb|ABB62876.1| suppressor of ftsH mutation [Shigella dysenteriae Sd197] (326 aa)
Score = 325, Expect = 2.1e-28, Identities = 99/290 (34%), Positives = 156/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VN K+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +  +T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNSKLCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDSTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQRRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|114771661|ref|ZP_01449065.1| putative Pseudouridine synthase, Rlu [alpha proteobacterium HTCC2255] >gi|114547733|gb|EAU50623.1| putative Pseudouridine synthase, Rlu [alpha proteobacterium HTCC2255] (341 aa)
Score = 325, Expect = 2.2e-28, Identities = 99/285 (34%), Positives = 149/285 (52%)
  Q:    10 LVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEES--EIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTR----------------TVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----------PKHINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +V ++ +LSRS     I    VT+ G+ I+K   K    S   I++     V++ +   P    ++IV+ED +++IVNKP  ++VHP     + TL N + Y FD       G+  R GIVHR+DK T GL++VAKS  +     K F D  I ++YLA+     Q                   + V   I R +T  +R        + A T    +  + +  L E  L TGRTHQIRVH   I + +I DPIYG           P+ +     +  Q L A  + FIHP T++ +N + D+P +  E I+
  S:    26 VVPAEVTLSRSRITKLIAEGAVTLAGEPITKLKYKAPAGSIFRIVMPP---VQDYENAQPENIPLDIVFEDDHLIIVNKPAGMVVHPAPGSENGTLVNALLYYFDGNLSGVGGEK-RPGIVHRIDKDTSGLLVVAKSDSAHAGLAKQFADHSISRRYLAVSKGVPQKSDPRLAGLRGVNFEDGGVIRVATNIARHKTDRKRMAVVQDAGRHAITRATVLENFAHSALMECWLETGRTHQIRVHFSHIGHGLIGDPIYGLRKAMPGSVFEPEDMVIVKGFSRQALHAKSIGFIHPITKEYMNFDSDIPSDLIELIE 336
>gi|40889481|pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna Pseudouridine Synthase Rlud (349 aa)
Score = 325, Expect = 2.2e-28, Identities = 101/290 (34%), Positives = 151/290 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+I+NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL +VAK++ +     +    ++I ++Y A+   H  T    VD PI R  T  R   +     K A T ++    ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E   +  +P++  E I+
  S:    41 QRLDQALAEXFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLXVVAKTVPAQTRLVESLQRREITREYEAVAIGH-XTAGGTVDEPISRHPTK-RTHXAVHPMGKPAVTHYRIXEHFRVHTRLRLRLETGRTHQIRVHXAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATXLRLYHPISGIEXEWHAPIPQDXVELIE 333
>gi|13473214|ref|NP_104781.1| pseudouridine synthase [Mesorhizobium loti MAFF303099] >gi|14023962|dbj|BAB50567.1| pseudouridine synthase [Mesorhizobium loti MAFF303099] (329 aa)
Score = 324, Expect = 2.4e-28, Identities = 102/289 (35%), Positives = 156/289 (53%)
  Q:     5 QRLDILVSSKF--SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQ----KIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREV---SRDIDAKEARTIF-------KEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG------------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  +++     +SRS  +  I    V+V+GK   +   K+     + +     + E +   P  + I  +++YED  ++++NKP  ++VHP + + + TL N +I +  DS  +   G   R GIVHRLDK T G+++VAK+  +  A ++ F D      +E+ YLAL+    Q  T  VDAP+ R     RR V    RD DA+ A T F       +   ++   +L E  L TGRTHQIRVH   I + VI DP YG     K  +              Q L A+ L F HP T   +     +P++ +E +
  S:    11 QRLDQWLAASLGPDMSRSRVQMLIRQGAVSVDGKPADETKRKMSAGESVSIA----MPEPEPAAPQGEAIALDVLYEDDALIVINKPAGLVVHPGAGNWTGTLVNALIHHCGDS--LSGIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKALSEAFADHGRTGDLERAYLALVWGIPQRPTGTVDAPLGRAADRVRRAVVPEGRD-DARHAVTHFAVQERFGENQQEFATASLVECRLETGRTHQIRVHMAHIGHPVIGDPDYGQAFRTKANRLPEPLKSQVKAFSRQALHAWLLAFRHPDTHLTMRFEAPIPRDMEELV 323
>gi|110833337|ref|YP_692196.1| pseudouridylate synthase [Alcanivorax borkumensis SK2] >gi|110646448|emb|CAL15924.1| pseudouridylate synthase [Alcanivorax borkumensis SK2] (323 aa)
Score = 324, Expect = 2.4e-28, Identities = 91/289 (31%), Positives = 154/289 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QR+D + +  F   SRS  +  I+N ++TVNG   +KP  K+     + L+ E  +E      P   D+++VY+D  ++++NKP  ++VHP +     TL N + ++ +    + N  P R GIVHRLD+ T GL++VA+SL++  +      D+ + ++Y A+    + T   +VDAP+ R     +++       K A T ++ +++Y+  T  +V+L TGRTHQIRVH       ++ DP+YG     P    +  +        Q L A KL  IHP   +      ++P +    I
  S:    22 QRVDQVAAELFEGFSRSRLQTWIKNGVLTVNGAQ-TKPKEKLTGNESLTLEVE--IEPELDDQPQSIDLDVVYQDDDLIVINKPTGLVVHPAAGHADGTLLNGLLHLDE----RLNSLP-RAGIVHRLDRDTTGLMVVARSLEAHQSLVAQLQDKSLFRQYEAIAVG-VMTGGGKVDAPMGRHPVDRKKQAVVKTGGKNAVTHYRVLDRYRAHTRIQVQLETGRTHQIRVHMAHRNYPLVGDPLYGGRLKQPAGATEALRQALHKFPRQALHARKLGLIHPARGEYCEFQAELPADMTSLI 313
>gi|15792604|ref|NP_282427.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni subsp. jejuni NCTC 11168] >gi|86149976|ref|ZP_01068204.1| ribosomal large subunit pseudouridine synthases, RluA family [Campylobacter jejuni subsp. jejuni CF93-6] >gi|88596472|ref|ZP_01099709.1| ribosomal large subunit pseudouridine synthases, RluA family [Campylobacter jejuni subsp. jejuni 84-25] >gi|85839422|gb|EAQ56683.1| ribosomal large subunit pseudouridine synthases, RluA family [Campylobacter jejuni subsp. jejuni CF93-6] >gi|88191313|gb|EAQ95285.1| ribosomal large subunit pseudouridine synthases, RluA family [Campylobacter jejuni subsp. jejuni 84-25] >gi|112360598|emb|CAL35395.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni subsp. jejuni NCTC 11168] (322 aa)
Score = 324, Expect = 2.5e-28, Identities = 92/285 (32%), Positives = 162/285 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYN-GDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY-----LVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           RLD+ ++ K + SR+     IE + V VN KI  K + K+     I +   K+  E K       DI+++YED+ +L++NKP++++VH  S   S   A ++ ++ + K    N G  +R G+VHRLDK T G +++AK+  +    ++   D+ + + YLAL+   L+   + V+  + R  ++  ++++ D +   +K A++ F  + K +N TL   +LFTGRTHQIR H   +  +++ D +YG K        G+Y     L AY L FIHP T++++ +   + ++FK
  S:    11 RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISIASLKLCNEIKPQFEVDFDIDVLYEDEDLLVLNKPSNLVVHGAS---SVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINVVKTENLTLMAAKLFTGRTHQIRAHLASLNRYILGDSLYGYK--------GKYDCRIMLHAYFLYFIHPKTKEQIFVKAPLMEDFK 293
>gi|170017468|ref|YP_001728387.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum KM20] >gi|169804325|gb|ACA82943.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum KM20] (307 aa)
Score = 324, Expect = 2.5e-28, Identities = 91/288 (31%), Positives = 156/288 (54%)
  Q:     4 TQRLDILVSSK-FSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           T R+D +++ K    SR++    +++  + VN   + K + KV+   ++I      V+ T+++      ++I+YED  +L+VNKP  ++VHP +   S TL N + Y      I  NG   R GIVHR+D+ T GL++VAK+  +  A ++     K E+ Y AL+       +  ++AP+ R +   R++ +     +EA T F+ + +Y  +TL ++ L TGRTHQIRVH  +I + +I DP+YG  + +   T  GQ L A  L    P T + +  + ++P  F +
  S:    13 TGRIDAVLAKKSLPYSRTVLAEWLQDGHIVVNQTQV-KRSYKVNS-GDLITILPPAVQNTEIIAE-NMPLDIIYEDNDLLVVNKPQGMVVHPAAGHTSGTLVNALLYHAPLSTI--NGS-FRPGIVHRIDRDTSGLLMVAKNDKAHQALSEQLKAHKNERIYYALVRGEFSEDSGTINAPLARHKVD-RKKQAVQAGGREAITHFEVVTRYVGYTLLKIRLETGRTHQIRVHMTYIGHPIIGDPVYGSAQKLPHVTLNGQMLHAKTLSLTQPTTGELLTFDSELPSYFTK 295
>gi|113460513|ref|YP_718577.1| 23S rRNA pseudouridine synthase D [Haemophilus somnus 129PT] >gi|112822556|gb|ABI24645.1| ribosomal large subunit pseudouridine synthase D [Haemophilus somnus 129PT] (321 aa)
Score = 324, Expect = 2.5e-28, Identities = 102/285 (35%), Positives = 159/285 (55%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYGQYLVAYK--------LKFIHPFTQKEVNINLDMPKEF 289
           QRLD  ++  F   SRS  K  IE +LV VNG+II+   TKV     + L  E  +EE     P    + IVYED++IL++NKP D +VHP + +   T+ N + Y +   KI    +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+  +VD P+ R  T  R +++     K A T ++ + +++N+T   + L TGRTHQIRVH   I + ++ D  YG     PK  N + ++ Q +  +K        L+  HP T + +     +P +F
  S:    14 QRLDQTLAELFPDYSRSRLKTWIEGDLVKVNGEIINVARTKVYGGELVELCVE--IEEESRFEPENLPLNIVYEDEHILVINKPKDFVVHPGAGNQRGTVLNALLYHY--PKIV---EVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVQDLQKRKIIREYEAVAFG-VMTQGGKVDQPMSRHPTK-RTQMAVHPLGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHISHPLLGDQTYGGRPRPPK--NASEEFMQVMRDFKRQALHAIMLRLTHPITGEIMEWEAPLPDDF 301
>gi|188590369|ref|YP_001921578.1| ribosomal large subunit pseudouridine synthase D [Clostridium botulinum E3 str. Alaska E43] >gi|188500650|gb|ACD53786.1| ribosomal large subunit pseudouridine synthase D [Clostridium botulinum E3 str. Alaska E43] (302 aa)
Score = 324, Expect = 2.5e-28, Identities = 93/278 (33%), Positives = 154/278 (55%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIE--IVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN-FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           SRS  +  IE   + VN K+I K N K+    EI++     + E ++L    +DI+  I+YEDK +++VNK   ++VHP   + + TL N +  +F    +      +R GIVHR+DK T G++++AK+ +S N       D  + ++Y AL+    +  +  +D P+ R +   R +++   D + A T ++ + +Y    TL + +L TGRTHQIRVH   + + ++ DP+YG K      K GQ L A KL FIHP   + +    ++P+ F+E I+K
  S:    29 SRSFIQGLIEKESIKVNNKLI-KSNYKLKACDEIVIT----MPEAEILKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNAL--LFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFKNDSGVIDKPLGR-DKKNRLKIAITEDGRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRVHMASLGHPLVGDPLYGFKKQRFKLK-GQMLHAKKLGFIHPTKNEYMEFETNLPEYFEEIIEK 300
>gi|187931810|ref|YP_001891795.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. mediasiatica FSC147] >gi|187712719|gb|ACD31016.1| ribosomal large subunit pseudouridine synthase D [Francisella tularensis subsp. mediasiatica FSC147] (332 aa)
Score = 324, Expect = 2.5e-28, Identities = 99/284 (34%), Positives = 167/284 (58%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILK----EEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           +R+D+ ++ +F   SR+  +  ++   +TVNG+  +KP   V  DEE EI ++     E I E+         +++I++ED  I++++KP ++IVHP + + + T++N + + + D  K+       R GIVHRLDK T GL++ AKS  +++   +   ++K+ +KYLA++   +  +   ++ PI R + + R +++ +   KEA T +  I  Y  FTL E +L TGRTHQIRVH + IK+ ++ D  Y  K + K  K        Q L AYKL FIHP   K V     +P++
  S:    23 KRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRA-TKPKHIVLGDEEVEINIELLPTNEWIAEDI--------NLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLP------RAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGT-INQPIGR-DPTNRTKMAINYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYN-KSLTKLEKLAITIPTRQALHAYKLSFIHPTIAKMVKFKSKLPED 302
>gi|126664287|ref|ZP_01735278.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria bacterium BAL38] >gi|126623707|gb|EAZ94404.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria bacterium BAL38] (346 aa)
Score = 324, Expect = 2.5e-28, Identities = 94/279 (33%), Positives = 155/279 (55%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID--AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           +R+  +   EN  + VN  +  K N KV     + L       E ++LTP    ++IVYED  +L++NKP  ++VHP   + S TL N + Y F++  +  +  P   G+VHR+DK T GL++VAK+  +    +K F ++  E++Y+AL+  +++     V+  I R +T+  R    + D   K A T +K + ++   TL   +L TGRTHQIRVH + I + + ND  YG   I K T + +Y               L A  L F HP T++ +  N  +P++ ++ I+K+
  S:    43 TRNKIQQAAENGSILVN-DVAVKSNYKVKAGDVVRLVLAHPTYE-QLLTPENIPLDIVYEDDQLLVINKPAGMVVHPGHGNYSGTLVNALAYHFENLPMNSSERP---GLVHRIDKDTTGLLVVAKTELAMAYLSKQFAEKTSEREYVALVWGNIEEDEGTVEGNIGRHDTNRMRMAVHESDEKGKPAVTHYKVLERFGYVTLVSCQLETGRTHQIRVHMKHIGHTLFNDERYGGDSILKGTTFTKYKQFVDNCFKVLPRQALHAKTLGFEHPITKEFLRFNTPIPQDLQDCIEKW 333
>gi|75909134|ref|YP_323430.1| ribosomal large subunit pseudouridine synthase D [Anabaena variabilis ATCC 29413] >gi|75702859|gb|ABA22535.1| ribosomal large subunit pseudouridine synthase D [Anabaena variabilis ATCC 29413] (312 aa)
Score = 324, Expect = 2.6e-28, Identities = 91/288 (31%), Positives = 148/288 (51%)
  Q:     2 KNTQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIIS--KPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID--AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           +N+ R+D  ++ +   LSRS  +  IE   V VNGK+ +  K N KV +   + + E + +E      P    ++I+YED  +LI+NKP  ++VHP       TL N +  +     +   G   R GIVHRLDK T G + +AK+  ++         +   ++YL +++   +T + +VD PI R     ++     ++   + A T ++   +  NFTL   +L TGRTHQIRVH+  I + ++ DP+YG          GQ L A++L+  HP T   V +    P+ F
  S:    11 ENSARIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVGDRITLEVPEAQPLELQAEDIP----LDILYEDDQLLILNKPAGLVVHPAPGHSHGTLVNAL--LAHCPHLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQTKTARREYLGVVYGAPKTSSGKVDLPIGRHPQDRKKMAIVPVEEGGRSAITHWQIQERLGNFTLIHFQLETGRTHQIRVHSAKIGHPIVGDPVYGSGRSVGVNLPGQALHAWRLRLQHPITGDWVEVTATPPQSF 297
>gi|89898789|ref|YP_515899.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila felis Fe/C-56] >gi|89332161|dbj|BAE81754.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila felis Fe/C-56] (330 aa)
Score = 324, Expect = 2.7e-28, Identities = 100/288 (34%), Positives = 162/288 (56%)
  Q:     3 NTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKV---DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           N  RLD  LVS     SR+  +  I +  VTVN ++ +K  T++   D  S II ++E+++E      P  K    VYED+ IL++NKP D++VHP    +  T+ + ++  I +  K ++  +P R GI+HRLDK T GL+I AK+  +   +++LF  ++++K YLA+     +     +   + R   S R+E++  +  KEA T  + +      +L  +   TGRTHQ+RVH + +   ++ DP+YG   IN    YG   Q L AY L FIHP T + +N+  ++P + K
  S:    15 NRDRLDKFLVSQNPEYSRAFYQQHILDERVTVNEQVQTKVATQLVPGDSVSIIIEEKEELLELLPEAIPLDK----VYEDEMILVINKPRDMVVHPAPGHIRGTVVHALLHEIGERLKQEFPEEPWRPGIIHRLDKDTSGLLITAKTRQAKTIYSELFATKQLKKSYLAICVG--KPTATLIHTKLAR-HHSKRKEMAVSLTGKEAITHCEVLAYNGKLSLVLLRPETGRTHQLRVHMKHLNTPILGDPVYGSPSIN--AGYGLDKQQLHAYSLDFIHPQTHRRLNLTTELPCDMK 301
>gi|57167607|ref|ZP_00366747.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Campylobacter coli RM2228] >gi|57020729|gb|EAL57393.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Campylobacter coli RM2228] (321 aa)
Score = 323, Expect = 3.3e-28, Identities = 95/290 (32%), Positives = 159/290 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDI---DAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY-----LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLDI ++     SR+     IE N V VN KI +K + K+    +++L    +VEE K       DIEI+YED+ +L++NKP++++VH      S TL + +  I     +   G  +R G+VHRLDK T G +++AK+  +    ++   D+ + + YLAL+   L+   + +D  + R   +  +++  +     +KEA++ F  + K +  +L   +LFTGRTHQIR H   I  H++ D +YG +        G+Y     L AY L FIHP   +++ I   +  +FK+ ++K
  S:    11 RLDIFLAKNLQQSRNQIASMIEKNCVWVNDKIQNKNSFKLKVGDKLVLNL-PLVEEAKPKFDIDFDIEILYEDEDLLVLNKPSNLVVHGAKSVRSATLVDWL--IEKQYTLSTLGGEVRAGLVHRLDKETSGAILIAKNNFTHQKLSEQLSDKTMGRIYLALIDLPLKEDKIIIDKALIRSSANAIKKIVTNSFVKGSKEAKSAFVNLAKSEEVSLIGAKLFTGRTHQIRAHLASINRHILGDELYGYR--------GKYECRIMLHAYFLYFIHPRNGEKIFIQAPLMDDFKQILEK 297
>gi|86150741|ref|ZP_01068957.1| RluA [Campylobacter jejuni subsp. jejuni 260.94] >gi|85841911|gb|EAQ59157.1| RluA [Campylobacter jejuni subsp. jejuni 260.94] (322 aa)
Score = 323, Expect = 3.4e-28, Identities = 92/285 (32%), Positives = 162/285 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYN-GDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY-----LVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           RLD+ ++ K + SR+     IE + V VN KI  K + K+     I +   K+  E K       DI+++YED+ +L++NKP++++VH  S   S   A ++ ++ + K    N G  +R G+VHRLDK T G +++AK+  +    ++   D+ + + YLAL+   L+   + V+  + R  ++  ++++ D +   +K A++ F  + K +N TL   +LFTGRTHQIR H   +  +++ D +YG K        G+Y     L AY L FIHP T++++ +   + ++FK
  S:    11 RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISIASLKLCNEIKPQFEVDFDIDVLYEDEDLLVLNKPSNLVVHGAS---SVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGSILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINVVKTENLTLMAAKLFTGRTHQIRAHLASLNRYILGDSLYGYK--------GKYDCRIMLHAYFLYFIHPKTKEQIFVKAPLMEDFK 293
>gi|50842255|ref|YP_055482.1| pseudouridylate synthase [Propionibacterium acnes KPA171202] >gi|50839857|gb|AAT82524.1| pseudouridylate synthase [Propionibacterium acnes KPA171202] (306 aa)
Score = 323, Expect = 3.4e-28, Identities = 85/286 (29%), Positives = 149/286 (52%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPT-SYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +R+D+  +    +SRS     IE+  V ++G+ +S+ + +V     + +     V    +     + + I+++D  I++V+KP  +  HP+  ++  + + ++    F    I  +G P R GIV RLD  T GL++VAKS  ++    + F D+ ++K YLAL+  H    T  +DAPI R      +    D   + + T ++ +  +++ TL +V L TGRTHQIRVH   IK+    DP+YG  P    +     Q+L A +L F HP + + V  + D+P + +
  S:    13 ERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLCDPVATPSITPRIVEGMRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGF---AISTSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMAIVD-GGRHSVTHYETVEAFRHATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLYGCDPALAKELGLERQWLHAGELSFTHPGSGEWVTFHADLPADLQ 297
>gi|15895383|ref|NP_348732.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824] >gi|15025103|gb|AAK80072.1|AE007712_8 Predicted pseudouridylate synthase, YLYB B.subtilis ortholog [Clostridium acetobutylicum ATCC 824] (305 aa)
Score = 323, Expect = 3.5e-28, Identities = 96/289 (33%), Positives = 156/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIIS---KPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QR+D+ ++ +F ++SRS  +  I    V VNGK +    K  ++ + E EI   EE  +E   +       ++IVYED+ I++VNK   ++VHP   + + TL N +  ++  K +      LR GIVHR+DK T G+++VAK+  +         +  + + Y A++   ++     VD P+ R     R +++     + A T +K + +Y+N TL E +L TGRTHQIRVH  +I + ++ DP+YG K   +    GQ L A KL FIHP   K +    + P  F++ I
  S:    15 QRIDVYLAQEFENISRSHIQDLIGKKKVFVNGKAVKSNYKLKSRDNVEFEIPDNEELKIEAENI------PLDIVYEDRDIVVVNKAQGMVVHPAPGNYNGTLVNAL--LYHCKDLSGINGVLRPGIVHRIDKDTSGILVVAKNDAAHKNLANQLKEHSMNRVYRAVVEGIIKEDEGTVDKPLAR-HPVERVKIAVVKGGRNAVTHYKVLERYRNSTLIECKLETGRTHQIRVHMAYIGHALVGDPLYGYKK-QRFNLEGQMLHAQKLGFIHPTKGKYMEFEREAPSHFQKII 297
>gi|187932847|ref|YP_001886621.1| ribosomal large subunit pseudouridine synthase D [Clostridium botulinum B str. Eklund 17B] >gi|187721000|gb|ACD22221.1| ribosomal large subunit pseudouridine synthase D [Clostridium botulinum B str. Eklund 17B] (302 aa)
Score = 322, Expect = 4.3e-28, Identities = 92/278 (33%), Positives = 152/278 (54%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN-FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           SRS  +  IE   + VN K+I K N K+    EI++   +   ET  +     D++I+YEDK +++VNK   ++VHP   + + TL N +  +F    +      +R GIVHR+DK T G++++AK+ +S N       D  + ++Y AL+    +  +  +D P+ R +   R +++   D + A T ++ + +Y    TL + +L TGRTHQIRVH   + + ++ DP+YG K   K    GQ L A KL FIHP   + +    ++P+ F+E I+K
  S:    29 SRSFIQGLIEKESIKVNDKLI-KNNYKLKACDEIVITMPE--AETLKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNAL--LFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFKNDSGIIDKPLGR-DKKNRLKIAITEDGRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRVHMASLGHPLVGDPLYGFKK-QKFKLKGQMLHAKKLGFIHPTKNEYMEFETNLPEYFEEIIEK 300
>gi|8575702|gb|AAF78056.1|AF263561_1 23S rRNA pseudouridine synthase [secondary endosymbiont of Glycaspis brimblecombei] (314 aa)
Score = 322, Expect = 4.4e-28, Identities = 96/284 (33%), Positives = 155/284 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKY---------GQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  ++  F   SRS  K  I +N V VNGKII++P  KV    +I +  + ++EE     P    + IVYED  I+++NKP D++VHP + +   T+ N + Y +         +  R GIVHRLDK T GL+++AK++ +     +    ++I ++Y A+++  + T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L +GRTHQIRVH   I + ++ DP+YG  P+ +   ++           Q L A  L+  HP T  E+  + D+P +
  S:     7 QRLDQTLAELFPDYSRSRIKEWILDNRVQVNGKIINRPKEKVFGSEQIAI--DVLIEEDMRWQPQNIPLNIVYEDDEIIVINKPRDLVVHPGAGNPDGTVLNALLYRYPEII-----NVPRAGIVHRLDKDTTGLMVIAKTIPAQTHLVEALQLREITREYEAVVNGRM-TAGGTVDEPIARHPTK-RTHMAIHPLGKPAITHYRVMEHFRAHTRLRLRLESGRTHQIRVHMAHINHPLVGDPVYGGRPRPLKGVSEEFRQVMNNFDRQALHATMLRLYHPRTGIEMEWHADIPAD 293
>gi|78485714|ref|YP_391639.1| pseudouridine synthase, RluD [Thiomicrospira crunogena XCL-2] >gi|78364000|gb|ABB41965.1| ribosomal large subunit pseudouridine synthase D [Thiomicrospira crunogena XCL-2] (352 aa)
Score = 322, Expect = 4.6e-28, Identities = 94/292 (32%), Positives = 157/292 (53%)
  Q:     2 KNTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKV-DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYGQYLVAYK--------LKFIHPFTQKEVNINLDMPKEFKEYI 293
           K   RLD +++  FS  SR+  +  I   LVT++G    KPN KV  +ES ++L E   +E+          IE+VYED+ IL++NKP  ++VHP + +   TL N + + +++ +     +  R GIVHRLDK T GL++VAK++ +     +      +E+ Y A++   + +    +  PI R  T  +R     +  K A + ++ + +++  T   V+L TGRTHQIRVH  ++   ++ DP+Y      P+ +    ++  YL  +K        L   HP T K +   + MP +  E I
  S:    14 KMGHRLDAVLAELFSDYSRNRIQDWIRAGLVTLDGVEHKKPNFKVFGDESVVLLAE---IEDEVSYQAQDIPIEVVYEDEDILVLNKPAGLVVHPGAGNPDGTLLNALLFHYETIR-----EVPRAGIVHRLDKETSGLMVVAKNVPAQTHLVEQLQQHDVERVYDAIVVGKMISGGT-ISKPIGRHPTDRKRMAVLTVGGKPATSHYRVLERFREHTHVRVKLETGRTHQIRVHMAYLGFPLVGDPVYAGRLRIPQQM--MPEFADYLRGFKRQALHAGQLSLTHPRTGKTMKWKVSMPDDMLELI 309
>gi|12045061|ref|NP_072871.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37] >gi|66880194|ref|ZP_00405178.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Mycoplasma genitalium G-37] >gi|1351510|sp|P47451|Y209_MYCGE Uncharacterized RNA pseudouridine synthase MG209 (RNA-uridine isomerase) (RNA pseudouridylate synthase) >gi|3844807|gb|AAC71427.1| pseudouridine synthase, RluA family [Mycoplasma genitalium G37] >gi|166079007|gb|ABY79625.1| pseudouridine synthase, RluA family [synthetic Mycoplasma genitalium JCVI-1.0] (308 aa)
Score = 322, Expect = 5.0e-28, Identities = 87/269 (32%), Positives = 154/269 (57%)
  Q:    26 IENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETS-TRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           I N  + VN K+  K +  V  D+  ++ + +E   +    + P+   +E+++EDK ++++NKP+ ++ HPT+++   +L  +   IF + K     +P+ +  VHRLD+ T G ++V K+  S         ++ +++ Y+AL+H      T  ++AP+ RV  +    ++++   AK+A T FK IN+ +   L  +EL TGRTHQIRVH +FI++ V NDP+YG K   K   YGQ+L A ++ FIHP   K ++ +  +  +F   +K
  S:    32 IMNGQIKVNEKLTFKNSLIVAKDDVIKVEIHDETTSDFITSVEPYNLKLEVLFEDKDLMVINKPSGLLTHPTTFNEKASL--LAACIFHNNK-----NPVYL--VHRLDRDTSGAIVVCKNQASLLNLQNQLQNRTLKRYYVALVHFPFNALTGSINAPLARVNNNKVMFKIAQTAKAKQAITKFKVINQNEKAALISLELLTGRTHQIRVHLKFIQHPVYNDPLYGIKS-EKKDSYGQFLHANRICFIHPTLNKPMDFHAPLEPKFSTKLK 293
>gi|196193269|gb|EDX88228.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881] (324 aa)
Score = 322, Expect = 5.0e-28, Identities = 92/289 (31%), Positives = 154/289 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QR+D + +  F   SRS  +  I+N ++TVNG   +KP  K+     + L+ E  +E      P   D+++VY+D  ++++NKP  ++VHP +     TL N + ++ +    + N  P R GIVHRLD+ T GL++VA+SL++  +      D+ + ++Y A+    + T   +VDAP+ R     +++       K A T ++ +++Y+  T  +V+L TGRTHQIRVH       ++ DP+YG     P    +  +        Q L A KL  IHP T +       +P +    I
  S:    22 QRVDQVAAELFDGFSRSRLQTWIKNGVLTVNGAK-TKPKEKLTGNESLTLEVE--IEPELDDQPQSIDLDVVYQDDDLIVINKPTGLVVHPAAGHADGTLLNGLLHLDE----RLNSLP-RAGIVHRLDRDTTGLMVVARSLEAHQSLVAQLQDKSLFRQYEAIAVG-VMTGGGKVDAPMGRHPVDRKKQAVVKTGGKNAVTHYRVLDRYRAHTRIQVQLETGRTHQIRVHMAHRNYPLVGDPLYGGRLKQPAGATEALRQALHKFPRQALHARKLGLIHPATGEYREFEAPLPADMTGLI 313
>gi|160880488|ref|YP_001559456.1| RluA family pseudouridine synthase [Clostridium phytofermentans ISDg] >gi|160429154|gb|ABX42717.1| pseudouridine synthase, RluA family [Clostridium phytofermentans ISDg] (313 aa)
Score = 322, Expect = 5.1e-28, Identities = 94/291 (32%), Positives = 156/291 (53%)
  Q:     5 QRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY-------KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  L   +  +SRS  +  I+++LV +NG +I K N ++ E    IL  E     +  +      ++I+YED+ I+++NKP  ++VHP +   S TL N + Y    +    NG  +R GIVHR+D  T G+++V K+  S  +  +      I +KY AL++N  +     VDAPI R     ++      + K A T ++ +  +       + +   E  L TGRTHQIRVH   + + ++ D +YGP+  +K    GQ L A  L F+HP TQ+ +     +P+ F++ I+K
  S:    16 ERIDSFLAEFEEGISRSYIQKLIKDSLVKINGNVI-KANYRLKEGD--ILTYEVPQPVSLEIAAENIPLDILYEDEDIIVINKPKGLVVHPAAGHYSGTLVNALLYHCKDRLSGING-VMRPGIVHRIDMNTTGVLVVCKNDKSHQSIAEQLKVHSITRKYEALVYNSFKQTEGTVDAPIGRHPVDRKKMAINHKNGKNAVTNYRVLENFNLGYVHNQGYAHIECTLKTGRTHQIRVHMASLHHPLLGDDVYGPEK-DKFHLEGQALHARVLGFLHPTTQEYMEFEAPLPEYFQQLIEK 309
>gi|118581597|ref|YP_902847.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM 2379] >gi|118504307|gb|ABL00790.1| ribosomal large subunit pseudouridine synthase D [Pelobacter propionicus DSM 2379] (315 aa)
Score = 321, Expect = 5.4e-28, Identities = 98/289 (33%), Positives = 155/289 (53%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIY--GPKHINK---------TTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK---EYIK 294
           RLD+ +SS+  S +RS  +  IE+  + V+G+ + +P+ K+     I ++  + V    +  P    +E++YED  ++++NKP  ++VHP   + S TL N ++ +  D   I   G  LR GIVHRLDK T G+++VAK+  S  A +  F    I++ Y AL++   Q  +  ++  I R  T   R        K A T ++   +Y    L E+ L TGRTHQIRVH       ++ DP+Y  G +  N          TT   Q L A  L FIHP +   +  ++DMP +     EY++
  S:    13 RLDLFLSSQLASETRSTIQRLIESGNIMVDGREV-RPSLKLKGGESISIQLPEPVAARPL--PESIPLEVLYEDGDLIVINKPAGMVVHPGPGNSSGTLVNALLAHCTDLSGI---GGELRPGIVHRLDKGTSGVMVVAKNDRSHQALSAQFSVHSIKRIYQALVYGSPQQDSGRLEGQIGRHPTDRLRRSGLARQGKHAVTRWRVRGRYGRICLMELRLETGRTHQIRVHMSEAGFPLLGDPLYPDGGRFNNLTDPRLRKLITTLARQALHARTLGFIHPASGNYLEFSVDMPADMAALLEYLE 311
>gi|119476934|ref|ZP_01617215.1| Pseudouridine synthase, RluD [marine gamma proteobacterium HTCC2143] >gi|119449741|gb|EAW30978.1| Pseudouridine synthase, RluD [marine gamma proteobacterium HTCC2143] (318 aa)
Score = 321, Expect = 5.4e-28, Identities = 98/275 (35%), Positives = 151/275 (54%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKH-----INKTTKYG-QYLVAYKLKFIHPFTQKEVN 280
           RLD + +  F   SR+  +  I++  +TV+G+   K   K+  +S  +L+   +VE+ +       D++IVYED+ +L+VNKP  ++VHP S + S TL N ++ ++ D   +       R GIVHRLDK T G+++VAK+L + N+       + + + Y A++   L    V V A I R      +     I  KEA T ++ I ++ N       L TGRTHQIRVH   IK+ ++ DP+Y      PK      IN    +G Q L A KL  IHP + +EV+
  S:    19 RLDQIAAQLFPDYSRARLQIWIKSGELTVDGEA-KKSREKL--QSGELLELRAVVEDEERWDAESMDLDIVYEDEALLVVNKPAGLVVHPGSGNASGTLLNALLAHLPDIASVP------RAGIVHRLDKDTSGIMVVAKTLAAQNSLVNQLQARTVSRVYEAVVFGSLTGGGV-VRADIGRHPRQRTKMAVLAIGGKEATTHYRLIKRFNNHCHIRCMLETGRTHQIRVHMAHIKHALVGDPVYAGRPRIPKGASEELINGLRGFGRQALHARKLSLIHPLSNEEVS 296
>gi|85707640|ref|ZP_01038706.1| pseudouridine synthase D large subunit [Erythrobacter sp. NAP1] >gi|85689174|gb|EAQ29177.1| pseudouridine synthase D large subunit [Erythrobacter sp. NAP1] (317 aa)
Score = 321, Expect = 5.4e-28, Identities = 90/292 (30%), Positives = 148/292 (50%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREV---SRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHIN---KTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           RLD  ++    LSR+  +  I    V + GK ++  + KV E +   +    +VE         +DI  ++ +ED+ +++VNKP  ++VHP + +   TL N + +     ++   G   R GIVHR+DK T GL++VAKS  +       F +  + ++YLA+   H       ++  + R + + ++           K A T +K +       L E  L TGRTHQ+RVH   I + ++ DPIYG  PK +       K+  Q L A +L FIHP    E+  + D+P + +E I + G
  S:    16 RLDKALADATELSRARVQALIAEGAVEIAGKAVTSASVKVTENTPFRITVPAVVEAEA----QAQDIALDVAFEDEDLIVVNKPAGMVVHPAAGNPDGTLVNALLH-HCRGQLSGIGGVARPGIVHRIDKDTSGLLVVAKSDAAHEGLAAQFAEHSVHRRYLAVCGGHPSPAEGTINERLGRSDANRKKMAVLPKNSSRGKHAITHYKVLKPIGAAALIECRLETGRTHQVRVHCASIGHALLGDPIYGRTPKVLKPLLSQLKFARQALHAAELGFIHPILGSELRFSADLPADMQELIDELG 313
>gi|52307928|gb|AAU38428.1| RluA protein [Mannheimia succiniciproducens MBEL55E] (327 aa)
Score = 321, Expect = 6.7e-28, Identities = 99/289 (34%), Positives = 157/289 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKT------TKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  IE+ LV +NGK+ + P  KV   E+ EI ++    +E+     P    + IVYED  IL++NKP D +VHP + + + T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+   VD P+ R  T  R  ++     K A T ++ +  ++N+T   + L TGRTHQIRVH   I + ++ D  YG     PK+ ++           Q L A  L+  HP T + +  +  +P++F E +
  S:    20 QRLDQTLAELFPDYSRSRLKTWIEDELVLLNGKVANIPREKVYGGEQVEITVE----IEDENRFEPQNIPLNIVYEDDDILVINKPKDFVVHPGAGNPNGTVLNALLYHYPQIT-----EVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRALQKRKITREYEAIAFG-IMTKGGTVDEPMSRHPTK-RTLMAVHPMGKPAVTHYRVMEHFRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEEFMSVLRNFQRQALHAIMLRLEHPITGELMEWHAPLPEDFVELV 311
>gi|149200603|ref|ZP_01877608.1| 23S rRNA/tRNA pseudouridine synthase [Lentisphaera araneosa HTCC2155] >gi|149136305|gb|EDM24753.1| 23S rRNA/tRNA pseudouridine synthase [Lentisphaera araneosa HTCC2155] (323 aa)
Score = 321, Expect = 6.8e-28, Identities = 93/293 (31%), Positives = 165/293 (56%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIEN---NLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDA---KEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLV-AYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           QRLD  +S +    SR+  +  +++    LV    KI ++ +  V E   +  K  +  +E+ +L P   +++I+YED  IL+VNKP  ++VHP + + + TL N ++    D+     +G   R GIVHRLDK T G++IVAKS  + +  ++ F  + +EK Y+AL    ++     + + I R   S R+++    D+   KEA + +K +      TL ++++ TGRTHQIRVH   I + V+ D +YG + +++     ++++ A++ + IHP TQ+ +     +  +FK    K+G
  S:    20 QRLDRYISQQLPEYSRTFLQKSLKDGAFELVRSGAKINARMSENVIEGDFVHYKMPEEADESTLL-PEDIELDIIYEDDDILVVNKPAGMVVHPGAGNYTGTLVNALLGRDLDTFSAMDDGSS-RPGIVHRLDKETSGVIIVAKSAKNLDKLSRSFARRDVEKYYVALCRGTIRVGRDTITSHIGR-SRSNRQKMENTNDSNRGKEAISHYKVLADNNGATLVKLKIDTGRTHQIRVHMSGINHPVVGDKLYGVRRLDEKESPDRHILHAWRTRIIHPGTQEIMTFTAPLHDDFKSVCDKFG 318
>gi|159899422|ref|YP_001545669.1| RluA family pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779] >gi|159892461|gb|ABX05541.1| pseudouridine synthase, RluA family [Herpetosiphon aurantiacus ATCC 23779] (323 aa)
Score = 320, Expect = 7.3e-28, Identities = 96/289 (33%), Positives = 156/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGK--IISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD LVS+    LSR+  +  I +  + VNG+    S P  ++ ++ EI L   K  +      P    ++++YED  +L+VNK   ++VHP     + TL N + Y +    +  +GD LR GIVHRLDK T GL+++AK   +    T+  + +++ KKYLAL+  H +  T  +DAPI R   + R  +    + + A T ++ +     ++L    L TGRTHQIRVH  +    ++ND +YG +   +T  +G    +L AY L F  P T +  +  + +P E ++ +
  S:    19 QRLDRLVSANMPDLSRTYVQQLITDLHIRVNGRGAKASLP-VQIGDQIEIFLPLAKPTDIVAEDLP----LDVIYEDADVLLVNKAAGMVVHPAPGHTTGTLVNALLYRY--PHLTTSGD-LRPGIVHRLDKETSGLLVIAKHDQARMMLTEQQMARRMHKKYLALVEGHWREPTGTIDAPIGR-NPNNRLRMMVMPEGRYAVTHYQVLEVLGPYSLVRATLETGRTHQIRVHFSYRNRPILNDALYGHRKPKET--FGIERHFLHAYHLGFRLPSTGEWCSWEVPLPAELEKIL 302
>gi|161510965|ref|YP_089013.2| 23S rRNA pseudouridine synthase D [Mannheimia succiniciproducens MBEL55E] (324 aa)
Score = 320, Expect = 7.7e-28, Identities = 99/289 (34%), Positives = 157/289 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKT------TKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  IE+ LV +NGK+ + P  KV   E+ EI ++    +E+     P    + IVYED  IL++NKP D +VHP + + + T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+   VD P+ R  T  R  ++     K A T ++ +  ++N+T   + L TGRTHQIRVH   I + ++ D  YG     PK+ ++           Q L A  L+  HP T + +  +  +P++F E +
  S:    17 QRLDQTLAELFPDYSRSRLKTWIEDELVLLNGKVANIPREKVYGGEQVEITVE----IEDENRFEPQNIPLNIVYEDDDILVINKPKDFVVHPGAGNPNGTVLNALLYHYPQIT-----EVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRALQKRKITREYEAIAFG-IMTKGGTVDEPMSRHPTK-RTLMAVHPMGKPAVTHYRVMEHFRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEEFMSVLRNFQRQALHAIMLRLEHPITGELMEWHAPLPEDFVELV 308
>gi|82703097|ref|YP_412663.1| pseudouridine synthase, RluD [Nitrosospira multiformis ATCC 25196] >gi|82411162|gb|ABB75271.1| ribosomal large subunit pseudouridine synthase D [Nitrosospira multiformis ATCC 25196] (318 aa)
Score = 320, Expect = 8.1e-28, Identities = 90/271 (33%), Positives = 148/271 (54%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY-------LVAYKLKFIHPFTQKEVNINLDMPKE 288
           SRS  +  I    V+V+G   S P  KV    +I+L   +   ET    P    ++IV+ED  I+I++KP  ++VHP S +   TL N + +       + +G P R GIVHRLDK T GL++VAK+L++  +  +    + ++++YLAL+   + +    VDAP+ R     R  ++     KEART ++ + ++ + TL    L TGRTHQIRVH + + + ++ DP+YG K    ++   Q        L A+KL+  HP   + +     +P++
  S:    26 SRSRLQSWILEKRVSVDGAC-SLPRQKVWGGEKIVLSPARDPAET-AHEPEAIALDIVHEDHAIIIIDKPAGLVVHPGSGNWQGTLLNALLH----HSPQLSGIP-RSGIVHRLDKETSGLLVVAKTLEAQTSLVRQLQKRTVKREYLALVWGSVSSHG-RVDAPVGR-HPVQRTRMAVVASGKEARTRYEVLEQFTDCTLLRCGLETGRTHQIRVHMQSLGHPLVGDPLYGGKAKKGSSATMQLAAFPRQALHAHKLELTHPQNGQRMGWEAPLPED 294
>gi|37525235|ref|NP_928579.1| 23S rRNA pseudouridine synthase D [Photorhabdus luminescens subsp. laumondii TTO1] >gi|36784662|emb|CAE13562.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate synthase) (uracil hydrolyase) [Photorhabdus luminescens subsp. laumondii TTO1] (325 aa)
Score = 320, Expect = 8.3e-28, Identities = 99/290 (34%), Positives = 153/290 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKY---------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I ++ V VNGK+I+KP  KV    EI +  + I+EE     P    + IVYED  IL++NK  D++VHP + +   T+ N + Y +         D  R GIVHRLDK T GL+++AK++ +     +    ++I ++Y A+    + T    V+ PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG  P+ +   +            Q L A  L+  HP T  E+  + ++P +    IK
  S:    18 QRLDQALAELFPDYSRSRIKDWILDDRVQVNGKLINKPKEKVLGGEEIAI--DAIIEEDARWEPQNIALNIVYEDDDILVINKSRDLVVHPGAGNPDGTVLNALLYHYPEI-----ADVPRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAVATGRM-TAGGMVEEPISRHPTK-RTHMAVHPMGKPAITHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHISHPLVGDPLYGGRPRPLKGASDEFREVMRNFDRQALHATMLRLYHPITGIEMEWHAELPDDMVMLIK 310
>gi|167753888|ref|ZP_02426015.1| hypothetical protein ALIPUT_02173 [Alistipes putredinis DSM 17216] >gi|167658513|gb|EDS02643.1| hypothetical protein ALIPUT_02173 [Alistipes putredinis DSM 17216] (356 aa)
Score = 319, Expect = 9.0e-28, Identities = 91/266 (34%), Positives = 142/266 (53%)
  Q:    31 VTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRRE-VSRD-IDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           + VNGK  +K + KV     I L       E +++ P    +EI YED  +L+VNKP  ++VHP   + S TL N + Y   +  +   GD +R G+VHR+DK T GL+++AK+  +     K F D  I ++Y+AL+  + +     +   I R     ++  V  D  D K A T ++ + +Y   TL E  L TGRTHQIRVH ++  + +  D  YG   I K T + +Y               L A  L F HP T ++V    ++P++F+  + K+
  S:    66 ILVNGKP-AKSSYKVKPGDRISLVMPYPKREIEII-PENIPLEIPYEDDDLLLVNKPAGMVVHPGHGNYSATLVNALTYYLQNLPLFQEGD-MRAGLVHRIDKNTSGLLVIAKNERAHARLAKQFFDHTITRRYVALVWGNFEEDEGTITGNIGRSPKDRQKMWVFEDGSDGKHAVTHYRVLKRYGYVTLIECRLETGRTHQIRVHMQWKGHPLFGDERYGGDRILKGTTFNKYKQFIENCFAAMPRQALHAKSLGFQHPTTGEQVYFESELPEDFRTVLAKW 345
>gi|188585950|ref|YP_001917495.1| pseudouridine synthase, RluA family [Natranaerobius thermophilus JW/NM-WN-LF] >gi|179350637|gb|ACB84907.1| pseudouridine synthase, RluA family [Natranaerobius thermophilus JW/NM-WN-LF] (328 aa)
Score = 319, Expect = 9.4e-28, Identities = 90/290 (31%), Positives = 157/290 (54%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN---FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK-----HINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD+ +S +   LSRS AK  I NN V VN   +    +      +++  + ++++    L P    ++IVYED+Y+L+VNKP +++VHP + +  +T+ N +  ++  + +       R GIVHRLDK T GL++VAK  ++ +  ++   ++++ + YLAL+      +   +D PI R +   R++++     K A T  + +  ++N    +  +  L TGRTHQIRVH   +   ++ DP+Y  K      I+K    GQ L ++ L F HP  +K +     +P +    I K
  S:    26 RLDLYLSEQIEDLSRSKAKMLINNNSVMVNDNWVKASYSIT--SGDVVKVDTQLIQSEITLIPQSIPLDIVYEDEYLLVVNKPRNMVVHPGAGNYRDTMVNAL--LYHCQNLSDGTSYERPGIVHRLDKDTSGLLVVAKQNETHDILSEEIKNRRVARTYLALVIGDFSKKKATIDLPIGR-DPRNRKKMAVVHGGKRAITKVEMLRSFQNPEKISYLKCSLETGRTHQIRVHLSHLGYPLLGDPVYRGKTGKNVDIDKNLT-GQALHSFSLAFTHPVFKKTMVFRAPLPSDMMNLISK 318
>gi|73541038|ref|YP_295558.1| ribosomal large subunit pseudouridine synthase D [Ralstonia eutropha JMP134] >gi|72118451|gb|AAZ60714.1| ribosomal large subunit pseudouridine synthase D [Ralstonia eutropha JMP134] (403 aa)
Score = 319, Expect = 9.4e-28, Identities = 95/289 (32%), Positives = 158/289 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPL-----RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKY---KNF-TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +RLD L++  FS  SRS  +  IE+  V V+G++  +P   V   + I ++ +    E++   P    +++VYED  +L+++KP  ++VHP + + S T+ N +           + DP      R GIVHRLDK T GL++VA++L +     +    + +++ YLAL+   +      +DAPI R     TR  +      K +RT F+ +      ++F ++   +L TGRTHQIRVH E I + ++ DP+Y      + T+ GQ                L A+KL  +HP T K V+     P++ +  I
  S:    69 ERLDKLLARHFSEFSRSRLQQWIESGAVRVDGEV-RRPRDAVQMGNRIEVQPQA-APESQAFAPEDVALDVVYEDDALLVIDKPAGLVVHPAAGNWSGTVLNGL----------LHRDPTAAALPRAGIVHRLDKETSGLMVVARTLTAQTDLVRQLQARTVKRTYLALVWGRIYEEGT-IDAPIGRDPRERTRMAIVHTNSGKPSRTHFRTLATVPLGRSFVSMVRCQLETGRTHQIRVHFESIGHPLVGDPVY-----YRATQRGQRPAIRVPLPVPFERQALHAFKLGLVHPVTGKTVSWTAPPPEDLQALI 365
>gi|15889714|ref|NP_355395.1| ribosomal large subunit pseudouridine synthase D [Agrobacterium tumefaciens str. C58] >gi|15157624|gb|AAK88180.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Agrobacterium tumefaciens str. C58] (340 aa)
Score = 319, Expect = 9.4e-28, Identities = 99/288 (34%), Positives = 157/288 (54%)
  Q:     6 RLDILVSSKF--SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPL-------RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQ----KIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRD--IDAKEARTIFKEINKYKN-------FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG------------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           R+D+ +  +    LSRS  K  IE   V +NG+ +++P  KV     +    E ++ E +   P  +DI  ++ YED+ ++++ KP  ++VHP + + + TL N + Y        + GD L       R GIVHRLDK T G+++VAK+ ++       F D      +E+ Y A++    +T    VDA + R    T+R V  +   DA+EA T ++ + ++          ++ E  L TGRTHQIRVH   I + +I DP YG     K                 Q L AY L F HP T + +    DMP++ +E +
  S:    24 RIDVWLVGEVGSDLSRSRLKALIEQGAVLLNGQPVTEPKKKVHPGDRV----EIVMPEPEDPVPQGEDIPLDVEYEDEDLIVLVKPAGLVVHPGAGNWTGTLVNALIY--------HCGDSLSGIGGVKRPGIVHRLDKETSGVMVVAKNDNAHRHLAAQFADHGRTGPLERAYKAVVWGRPRTLRGTVDAALGRGTDRTKRAVKNEDSFDAREAITHYEVMERFHEKPDASCLASMVECRLETGRTHQIRVHMAHIGHPLIGDPEYGAAFRTKANLLDEPARSTVNRFPRQALHAYLLAFEHPRTGEVMEFETDMPEDMEELV 335
>gi|150015406|ref|YP_001307660.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB 8052] >gi|149901871|gb|ABR32704.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB 8052] (299 aa)
Score = 319, Expect = 1.0e-27, Identities = 98/290 (33%), Positives = 159/290 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTI--FKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           ++++ +S++   S S+ K    N+ V    ++++        E EII K +   +E++ + P K DI+IVYED+ IL+VNK   ++VHPT    S TLAN +I Y  +S      G    + +V RLD  T GL+I+AK+  S    +K   + K+EKKYLAL+H  ++ +   +D PI + E      + R +D +  R+I  +K + +Y   +L E +L TGRTHQIRVH   + + +  D +YG        K  Q L A+ L F  P + + +++  ++P + KE I K
  S:    22 KVELGLSTRLIRSASLGKRIFVNDEVVKMNRVLN--------EGEII-KIDLAKDESQDIAPEKMDIDIVYEDEDILVVNKKPFMVVHPTKSYQSGTLANGVINYFMES------GQNCIVRLVSRLDMNTSGLIIIAKNQFSHGMLSKEMSENKVEKKYLALVHGIMKEKQGTIDLPIYKPE-GIENGIRRVVDERGQRSITHYKVVEEYNESSLVECKLETGRTHQIRVHLSHLGHPIYGDTLYGDGDEEDLIKR-QALHAFGLDFKSPRSGEILSLRAELPDDMKELISK 297
>gi|188534767|ref|YP_001908564.1| Ribosomal large subunit pseudouridine synthase D [Erwinia tasmaniensis] >gi|188029809|emb|CAO97690.1| Ribosomal large subunit pseudouridine synthase D [Erwinia tasmaniensis] (325 aa)
Score = 319, Expect = 1.1e-27, Identities = 100/289 (34%), Positives = 152/289 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINK---TTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I +  +TVN  II KP  KV    +I +  E  +EE          + IVYED  IL++NKP D++VHP + +   T+ N + Y F +       D  R GIVHRLDK T GL++VAK++ +          ++I ++Y A+    + T    VD PI R  ++ R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK  ++   TT      Q L A  L+  HP +  E+  +  +P++  + I
  S:    18 QRLDQALAELFPDYSRSRIKEWILDRRITVNDTIIDKPKEKVLGGEQISIDAE--IEEEARWEAQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYHFPAI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGRM-TAGGTVDQPISR-HSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFITTLRAFDRQALHATMLRLYHPISGIEMEWHAPLPQDMVDLI 309
>gi|78776982|ref|YP_393297.1| pseudouridine synthase, RluD [Sulfurimonas denitrificans DSM 1251] >gi|78497522|gb|ABB44062.1| ribosomal large subunit pseudouridine synthase D [Sulfurimonas denitrificans DSM 1251] (323 aa)
Score = 319, Expect = 1.1e-27, Identities = 98/294 (33%), Positives = 156/294 (53%)
  Q:     2 KNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN---FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +  +RLD  ++S    SRS     I+  LV V+GK++S+   K+ +   +++K      E K       D+EI+YED  IL++NKP  + VHP       TL + +K+     ++       R GIVHRLDK T G +++AK+  +    +    D+ + + YLA+++  L+    EV  PI R  +  R +++     K A++ FK +  Y N     L   +L+TGRTHQIRVH E +  H++ D IY   PK   K+ +    L AY + FIHP +++ V+    + K  +EYI K
  S:    10 ETIERLDTFLTSILGQSRSQIAQLIKKELVQVDGKVVSRSGVKLKKNQVVLVKFPP--AEIKPALDIDFDVEILYEDDDILVINKPTGLTVHPAPSVKEATLVDWLKH--KGMRLSSLSGEERHGIVHRLDKGTSGAMVIAKNNSTHEFLSDQLQDKSMGRYYLAVINPPLKDELTEVIFPIAR-SSHNRLKMAPLEHGKYAKSAFK-VLAYSNDEANQLIACKLYTGRTHQIRVHLESLNRHIVGDHIYAQSPKQ-EKSERI--LLHAYIIYFIHPKSKERVSFVASLDKGMQEYIDK 299
>gi|117925422|ref|YP_866039.1| ribosomal large subunit pseudouridine synthase D [Magnetococcus sp. MC-1] >gi|117609178|gb|ABK44633.1| ribosomal large subunit pseudouridine synthase D [Magnetococcus sp. MC-1] (332 aa)
Score = 319, Expect = 1.2e-27, Identities = 88/287 (30%), Positives = 148/287 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNG-----DPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKT-------TKYGQY----LVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           QRLD  +   F  L+RS  +  I+   V V+ ++   P+ KV     II+   +   E     P +  +EI++ED++++++NKP  ++VHP +     TL N + Y   +    + G       +R GIVHRLDK T G+++ AK   +    ++ F  + I ++YLAL     Q     ++  I R      +    +   + A T +K +     F L    L +GRTHQIRVH   I + ++ DP+YG +H   +        ++ Q+    L A+ L FIHP T +E++     P +F++
  S:    21 QRLDKALCCHFPDLTRSTLQRWIKEERVIVDHEVAKLPSQKVRVGQHIIIYPSE--PEPSTALPEEIALEILFEDEHLIVLNKPAGMVVHPGAGVNHGTLVNALLYHCGTPDNPHGGLSGIGGVIRPGIVHRLDKETSGIMVAAKQDHAHIHLSRQFEQRTIGRRYLALTRGIPQPAQGRIEGAIGRHPIHRTKMAVVEQGGRAAATRYKVLEPLGQFALIRCRLESGRTHQIRVHMTHIGHPLVGDPLYGAQHKAPSHWPPLHRQRFDQFQRQALHAHTLTFIHPHTGEEMSFKRPPPADFRQ 322
>gi|170077579|ref|YP_001734217.1| 23S rRNA-specific pseudouridylate synthase [Synechococcus sp. PCC 7002] >gi|169885248|gb|ACA98961.1| 23S rRNA-specific pseudouridylate synthase [Synechococcus sp. PCC 7002] (308 aa)
Score = 318, Expect = 1.3e-27, Identities = 88/290 (30%), Positives = 148/290 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTV-EVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +RLD  ++ +   LSRS  +  IE   V +N        TK+     +ILK       T  L P   D++I++ED++ LIVNKP  ++VHP   + + TL + +      + +   G   R GIVHRLDK T G + +AK+  +          +   ++Y+ +++   +      ++API R     R++++ D   + A T ++ + +  N++L   +L TGRTHQIRVH+  + N +I DP+Y     +K    GQ L A KL   HP T + +     +P EF++ ++
  S:    15 ERLDQWLAQQLPELSRSRLQRLIEQGQVQLNEAPCQSKKTKLKVGDRLILKIP--APATMALAPEAMDLDILFEDEHFLIVNKPAGMVVHPAPGNYTGTLVHGL-LAHCGENLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDQAHQHLQAQIKAKTARREYMGIVYGCPRNDAAGTIEAPIAR-HKGDRKKMAVDETGRPAVTHWEIMERLGNYSLLYYKLETGRTHQIRVHSAHMGNPIIGDPLYTSNKFDKVKLTGQALHARKLIVKHPVTGETIEAIAPLPTEFEKLLQ 302
>gi|150399091|ref|YP_001322858.1| RluA family pseudouridine synthase [Methanococcus vannielii SB] >gi|150011794|gb|ABR54246.1| pseudouridine synthase, RluA family [Methanococcus vannielii SB] (297 aa)
Score = 318, Expect = 1.4e-27, Identities = 96/294 (32%), Positives = 161/294 (54%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKH--INKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           ++L   +S  F LS  + K   +   + VN K IS  +  V+ E   +     I      +   +  I ++YED+Y++I++KP +++VH T   +S TL+N I     S + K N    ++  V+RLD  T G++IVAK+  S    +K   +   EKKY+ +++ HL+ ++  +  P+   E   +RE+      KE++T +  I + KN +L E+ELFTG+THQIRVH   I N +I D +YG K   I++     Q L +  LKFIHP T++ ++   ++PK+ K  +++  K
  S:    18 KKLSDFLSEDFELSNKMIKKYDKEKKIFVNSKNISLKSKLVENEVVYV----NIDAGNNTIIAEEIPISVIYEDEYVMIIDKPKNMVVHETKNVVSGTLSNAI-----SNRQKVNNQNYKIRFVNRLDMDTTGILIVAKNPYSHYLISKQMDEGIFEKKYICVVNGHLRLKSGIISNPLDLGEDGIKRELKNT--GKESKTKYTVIEELKNASLLEIELFTGKTHQIRVHLSSIGNFIIGDELYGEKSDLIDR-----QALHSSSLKFIHPITKENMHFKSEIPKDIKNLVERLRK 297
>gi|88608012|ref|YP_506045.1| ribosomal large subunit pseudouridine synthase A [Neorickettsia sennetsu str. Miyayama] >gi|88600181|gb|ABD45649.1| ribosomal large subunit pseudouridine synthases, RluA family [Neorickettsia sennetsu str. Miyayama] (330 aa)
Score = 318, Expect = 1.5e-27, Identities = 90/290 (31%), Positives = 154/290 (53%)
  Q:     6 RLDILVSSKFSL-SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY--KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD+ +       SRS  KH I+ + +   GKI  +P+ +V    E  L +  +  E K    + + +++ YED  +L++ KP  ++VHP   +   TL NI+++ + ++K+  + D  R GIVHRLDK T G +IVAK+  +  + +++  +  I ++YLAL+H+   + + E+  PIKR     R+ +      K A T +  I +   +  +L    L +GRTHQIR+H + I   V+ D +YG             L AY L+F HPFT+K +   ++     + +++K
  S:    14 RLDVFLHRCLPFFSRSFIKHCIKGSRIESEGKIQLEPSRRVVVGEEYHLFDLPL--ERKPRHAFVQPLDVRYEDDCLLVIYKPAGLVVHPGIGNREQTLVNILEHHYPTEKLS-SLDSSRPGIVHRLDKDTAGFLIVAKTNPAHLSLSQMIKEGVIRREYLALVHSVPASLSGEIKKPIKR---GQRKMMIGRCSGKPALTYYGVIARTVDRKCSLVHCRLGSGRTHQIRLHMKSIGCPVVGDKLYGLNRDADLCAPHHALWAYSLQFRHPFTRKNMAFYIEPASIIQPFLEK 300
>gi|37519642|ref|NP_923019.1| pseudouridine synthase [Gloeobacter violaceus PCC 7421] >gi|35210633|dbj|BAC88014.1| glr0073 [Gloeobacter violaceus PCC 7421] (310 aa)
Score = 317, Expect = 1.5e-27, Identities = 91/287 (31%), Positives = 147/287 (51%)
  Q:     2 KNTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKV---DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           ++  RLD  ++ + + LSR+  +  I+  LV +N +   +P   V   D  +  I   E +  E + +      ++IVYED+ +++++KP  ++VHP      +TL N +  +   + +      LR GIVHRLDK T GL++VAK+  +          +   + YLA++       T  +DAPI R     R++++     + ART ++ + +  NFTL E  L TGRTHQIRVH       +  DP+YG   +  T   GQ L A++L F HP T + +     MP E
  S:    17 QSAMRLDRWLAEQVADLSRARIQALIDQGLVLLNNRP-CRPRDLVHSGDAVALTIPAPEPLAIEARPIA-----LDIVYEDEELIVIDKPRGLVVHPAPGHSDDTLVNAL--LAHCRNLSGINGVLRPGIVHRLDKDTTGLLVVAKTDRAHQHLQTQIQAKTARRDYLAIIAGAPAETTGTIDAPIGR-HPVHRQKMAVHPKGRPARTHWRVLERLGNFTLVEFSLQTGRTHQIRVHCLHKGWPIAGDPLYGSVKVPATLN-GQALHAFRLGFEHPVTGERLTFESPMPAE 297
>gi|17228018|ref|NP_484566.1| hypothetical protein alr0522 [Nostoc sp. PCC 7120] >gi|9957317|gb|AAG09315.1| hypothetical protein [Nostoc sp. PCC 7120] >gi|17129867|dbj|BAB72480.1| alr0522 [Nostoc sp. PCC 7120] (312 aa)
Score = 317, Expect = 1.6e-27, Identities = 92/288 (31%), Positives = 147/288 (51%)
  Q:     2 KNTQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID--AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           +++ R+D  ++ +   LSRS  +  IE   V VNGK+ +     +     I L+    V E + L    +DI  +I+YED  +LI+NKP  ++VHP       TL N ++ +  D   I   G   R GIVHRLDK T G + +AK+  ++         +   ++YL +++   +T + +VD PI R     ++     I+   + A T ++   +  NFTL   +L TGRTHQIRVH+  + + ++ DP+YG          GQ L A++L+  HP T   V      P+ F
  S:    11 EDSARIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVGDRITLE----VPEAQPLEIQAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHSHGTLVNALLAHCPDLPGI---GGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQAKTARREYLGVVYGAPKTASGKVDLPIGRHPQDRKKMAVVPIEEGGRSAITHWQIQERLGNFTLIHFQLETGRTHQIRVHSAKMGHPIVGDPVYGSGRSVGVNLPGQALHAWRLRLQHPITGDWVEATATPPQSF 297
>gi|50955140|ref|YP_062428.1| ribosomal large subunit pseudouridine synthase [Leifsonia xyli subsp. xyli str. CTCB07] >gi|50951622|gb|AAT89323.1| ribosomal large subunit pseudouridine synthase [Leifsonia xyli subsp. xyli str. CTCB07] (306 aa)
Score = 317, Expect = 1.7e-27, Identities = 90/285 (31%), Positives = 146/285 (51%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPT-SYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           R+D  ++     SRS A    E+  VTV+G+   K + ++   S + +  +   EE +++     ++ IV+ED  I++++KP  +  HP+  ++    L  +    F   +I  +G P R GIVHRLD  T GL++VAKS  ++    + F D+ +EK Y A++  H    T  +DAPI R   S  R  +     K + T ++ I  +   +L E+ L TGRTHQIRVH    ++  + D +YG  P    +     Q+L A +L F HP T + V      P +F+
  S:    16 RVDAGLAKLLGFSRSFAAEVAESGGVTVDGREAGKSD-RLPAGSWLDVTWQP-REEPRIVPIVVSELTIVHEDDDIVVLDKPAGVAAHPSIGWEGPTVLGALAAAGF---RISTSGAPERAGIVHRLDAGTSGLMVVAKSEHAYTVLKRAFHDRTVEKIYHAVVQGHPDPLTGTIDAPIGRHPKSDWR-FAVVAGGKPSVTHYETIEAFPAASLLEIHLETGRTHQIRVHMSAQRHPCVGDAMYGADPTLSARLGLTRQWLHAVQLAFAHPATGEWVTFTTAYPADFR 297
>gi|15966478|ref|NP_386831.1| putative ribosomal large subunit pseudouridine synthase protein [Sinorhizobium meliloti 1021] >gi|15075749|emb|CAC47304.1| Putative ribosomal large subunit pseudouridine synthase [Sinorhizobium meliloti 1021] (343 aa)
Score = 317, Expect = 1.7e-27, Identities = 97/288 (33%), Positives = 156/288 (54%)
  Q:     6 RLDILVSSKFS--LSRSIAKHKIENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQ----KIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDI--DAKEARTIFKEINKYKN-------FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG------------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD  ++   +   SR+  K  IE   V++NG  +++P  KV   +   I L E +  E      P    ++++YED  ++++ KP  ++VHP + + + TL N +I +  DS  +   G   R GIVHRLDK T G+++VAK+  +    +  F D      +E+ Y A++    +    ++DAP+ R    T+R V R+   DA+EA T ++ + +Y          +  E  L TGRTHQIRVH   I + +I DP YG     K                 Q L A+ L+F HP T + ++    +P + +E I
  S:    24 RLDAFLTEALAGEFSRNRIKSLIEQGAVSINGATVTEPKRKVHPGDSFRIALPEPEDPEPKGEAIP----LDVLYEDADLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCGDS--LSGIGGVKRPGIVHRLDKDTSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVWGRPRQLKGKIDAPLGRAGDRTKRAVKREDSDDAREAITHYEVVERYHEKPDGTSLASTVECHLETGRTHQIRVHMAHIGHPLIGDPDYGAAFRTKANLLPEPARAAVNRFPRQALHAFMLQFEHPATGETMHFETPVPADMQELI 335
>gi|15618629|ref|NP_224915.1| pseudouridine synthase [Chlamydophila pneumoniae CWL029] >gi|15836251|ref|NP_300775.1| pseudouridine synthase [Chlamydophila pneumoniae J138] >gi|16752321|ref|NP_444579.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila pneumoniae AR39] >gi|33242078|ref|NP_877019.1| ribosomal large subunit pseudouridine synthase A [Chlamydophila pneumoniae TW-183] >gi|4377023|gb|AAD18858.1| predicted Pseudouridine Synthase [Chlamydophila pneumoniae CWL029] >gi|7188966|gb|AAF37922.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila pneumoniae AR39] >gi|8979091|dbj|BAA98926.1| pseudouridine synthase [Chlamydophila pneumoniae J138] >gi|33236588|gb|AAP98676.1| ribosomal large subunit pseudouridine synthase A [Chlamydophila pneumoniae TW-183] (325 aa)
Score = 316, Expect = 2.1e-27, Identities = 94/294 (31%), Positives = 162/294 (55%)
  Q:     2 KNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +N+ RLD  L       SR+  +  I + LV +NG+I ++  T+++   +I+  + +  EE   L P    ++ VYED  IL++NKP D++VHP       TL + ++  I +  K ++  +P R GIVHRLDK T GL+I AK+  +   F++LF  ++++K YLA+     + R+  +   I R   + R+E++     KEA T  + +      +   +   TGRTHQ+RVH + +   ++ DP+YG   +N  + YG   Q L AY + F HP T++  ++   +P++ +  + K
  S:    12 ENSGRLDKYLTEVHPKYSRAFYQEHILSGLVQINGQINTRVATRLNC-GDIVTIDIQEKEELLELLPEAIPLDKVYEDGMILVINKPRDMVVHPAPGHFHGTLVHALLHEIGERLKEEFPEEPWRPGIVHRLDKDTSGLIITAKTRQAKKVFSELFSTKRLKKSYLAVCIG--KPRSTTIHTHISR-HQNKRKEMTVSSQGKEAVTHCQVLAFNGKLSFVALSPETGRTHQLRVHMKHLGTPILGDPVYGIPSMN--SSYGLDKQQLHAYSVDFTHPETRQFCSLKAGLPEDMRSLLIK 304
>gi|152993336|ref|YP_001359057.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp. NBC37-1] >gi|151425197|dbj|BAF72700.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp. NBC37-1] (317 aa)
Score = 316, Expect = 2.3e-27, Identities = 98/291 (33%), Positives = 162/291 (55%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEI-NKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQ-YLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           R+D +++ +  +SR+  +  +++ LV+VN K+++K + KV E  EI  + ++  +   V   +  D+EI+YED+Y+++VNKP+ ++VHP       TL + ++K       I  +G+  R GIVHR+DK T G +++AK        ++   D+ + + YLAL+ +H     V VD PI R     R ++      K A+T FK++     +  L   +LFTGRTHQIRVH   +  H++ D +YG K  +K  K  + YL AY L  IHP T  ++     +  + K Y+ KY
  S:    11 RIDKVLAHELDVSRNQVEKLVKDGLVSVNKKMVTKTSFKVVEGDEITYEFKEAEKREPVEIDF--DVEILYEDEYLMVVNKPSGLVVHPAPSVKEPTLVDWLVKKGISLSTI--SGEE-RHGIVHRIDKETTGALVIAKDNKVHEMLSEQLQDKSMGRYYLALI-DHFLKEDVVVDKPIGR-NPHNRLKMDVVPHGKPAKTAFKKLLTSEYDVELIAAKLFTGRTHQIRVHLNTLGRHILGDDLYGFK--SKRDKIPRVYLHAYLLYLIHPVTGVKMEFTAPLFDDMKLYLSKY 295
>gi|194366931|ref|YP_002029541.1| pseudouridine synthase, RluA family [Stenotrophomonas maltophilia R551-3] >gi|194349735|gb|ACF52858.1| pseudouridine synthase, RluA family [Stenotrophomonas maltophilia R551-3] (329 aa)
Score = 316, Expect = 2.4e-27, Identities = 95/290 (32%), Positives = 155/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKV-LTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R D +V+  F   SRS     I+N  V ++G   ++P   +     + L    +V ET+    P    +++++ED+Y+L++NKP  ++VHP + + S TL N + +   S  +     P R GIVHRLDK T G+++VAK+L++  A  +    + + ++YLA++   L       DAPI R     R ++    D KEA T ++   +++  T  E  L TGRTHQIRVH   I++ ++ DP+YG     PK  +            Q L A  L+F+HP T + V     +P +    +K
  S:    21 RRFDAVVAELFPEYSRSRLTEWIKNGDVLLDGAQ-ARPRDPLRGGEVVTLT---VVLETQTDAQPEDIPLDVLFEDEYLLVINKPVGLVVHPGAGNHSGTLVNALLFRDPSVAVL----P-RAGIVHRLDKDTSGVMVVAKTLEAQTALVEQLAARDVHRQYLAIVMGALVAGGT-ADAPIDR-HPRDRLKMGVREDGKEAVTHYRLRERFRAHTALECRLETGRTHQIRVHMAHIRHPIVGDPLYGGALKLPKGASDELVAALRGFKRQALHAETLEFVHPITGETVRNTAPVPADMLHLLK 312
>gi|77920540|ref|YP_358355.1| suppressor of ftsH mutation [Pelobacter carbinolicus DSM 2380] >gi|77546623|gb|ABA90185.1| ribosomal large subunit pseudouridine synthase D [Pelobacter carbinolicus DSM 2380] (326 aa)
Score = 316, Expect = 2.4e-27, Identities = 93/297 (31%), Positives = 159/297 (53%)
  Q:     2 KNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN--FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI----KKYGK 298
           ++ +RLD  LV     LSRS  K  I++  V ++G   +KP +K+   E   + + +    E      P    + I+YED+++++++KP  ++VHP       TL N +  +   + +   G  LR GIVHRLDK T G+++  K+  +  +    F    I ++Y+AL+H  L      +D PI R  T  ++  +     + A T ++ + ++ +   TL E+ L TGRTHQIRVH    ++ ++ DP+YG          P+ + +    G Q L A  L F HP T K +  +  +P++ +  I    +KYG+
  S:    13 RSPERLDRFLVEQLPELSRSQLKKLIDDGRVLLDGAA-AKPGSKLKGGETLTVDVPDPSPAEAVSEDIP----LVILYEDRHLIVIDKPPGMVVHPAPGHYQGTLVNAL--LHHCQDLSGIGGELRPGIVHRLDKDTSGVMVATKTDSAHQSLAAQFKAHSITRRYIALIHGVLTGDRGSIDRPIGRHPTHRKKMSTTCRTGRHAVTHWRVLRRFDDDRLTLVELALETGRTHQIRVHFSEQQHPLLGDPVYGGSGRLKTINDPQLLKRAKALGRQALHARLLGFQHPETGKYLEFSSPLPEDLRSVIDYLTEKYGQ 322
>gi|28211672|ref|NP_782616.1| ribosomal large subunit pseudouridine synthase D [Clostridium tetani E88] >gi|28204114|gb|AAO36553.1| ribosomal large subunit pseudouridine synthase D [Clostridium tetani E88] (226 aa)
Score = 315, Expect = 2.6e-27, Identities = 86/228 (37%), Positives = 136/228 (59%)
  Q:    71 DIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTI--FKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK----HINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           +++IVYED+ IL++NK   I+VHPT      TL+N I Y F+ K     G+   + +V RLD+ T GL+I+AK+  +  A  +       +K YLA++H  L  +   +D PI R E S+ + V   +D K  R+I  +K + ++K+ +L E  L TGRTHQIRVH E + + +I D +YG +    +IN+     Q L AYKL F HP T + + ++ D+P + K+ ++ + K
  S:     2 ELDIVYEDEDILVINKNPGIVVHPTKSHPRGTLSNGILYYFEDK-----GENCIVRLVSRLDRDTSGLIIIAKNQFAHMALARDMNKDTFKKFYLAIIHGKLTKKEGTIDLPIYRPEDSSLKRV---VDQKGQRSITHYKVVEEFKDASLVEFLLETGRTHQIRVHVEHLGHPIIGDSLYGNEDDTMYINR-----QALHAYKLVFPHPRTGEILELSCDIPSDIKDSMEIFKK 222
>gi|152997613|ref|YP_001342448.1| RluA family pseudouridine synthase [Marinomonas sp. MWYL1] >gi|150838537|gb|ABR72513.1| pseudouridine synthase, RluA family [Marinomonas sp. MWYL1] (327 aa)
Score = 315, Expect = 2.8e-27, Identities = 96/293 (32%), Positives = 160/293 (54%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           R D + +  FS  SRS  +  I+  ++ V+GKI +KP  K+     + L  + ++E  +       D+++VYED  I+I+NKP  ++VHP   +   TL N I+ +  ++  I       R GIVHRLDK T GL++VAK+L +         ++ + ++Y A+    +    V VD PI R   + +++    ++ K+A T ++ + ++KN T   ++L TGRTHQIRVH  FI+  ++ DP YG     PK  +   +        Q L A KL+  HP T + +   +D+P + K+ +    K
  S:    19 RFDQIATELFSDYSRSRIQSWIKEGVLKVDGKI-TKPKEKLFGGEVVTL--DIVIEAQEEHEAQAMDLDVVYEDDDIMIINKPAGLVVHPAVGNRDGTLMNAILHHAPETAHIP------RAGIVHRLDKETTGLMVVAKTLAAQTDLVMQLQERSMGREYEAVSIGVMTGGGV-VDEPIGRHPHNRQKQAVEPVNGKDAVTHYRLVERFKNHTHIRLKLETGRTHQIRVHMAFIQYPLVGDPQYGGRLKMPKACSPELQDELRHFRRQALHAKKLELSHPITGEWMEWEIDLPDDMKKLLDALKK 314
>gi|110601605|ref|ZP_01389784.1| Pseudouridine synthase, RluD [Geobacter sp. FRC-32] >gi|110547688|gb|EAT60935.1| Pseudouridine synthase, RluD [Geobacter sp. FRC-32] (319 aa)
Score = 315, Expect = 2.9e-27, Identities = 90/294 (30%), Positives = 160/294 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           +RLD  ++    +L+R+  +  +E+ ++TVNG +  KP+ K+    ++ +     VE      P    +EI+YED+ +++VNK   ++VHP + +   TL N ++ +  D   I   G  LR GIVHR+DK T G+++VAK+  S  A ++ F +  I++ Y+A+++   +T +  +++ I R     +R   +    K A T ++ I +Y    L  + L TGRTHQIRVH     + ++ D +YG          P       + G Q L A  L F+HP T++ +  + D+P++    ++   K
  S:    15 ERLDSYIARTVETLTRAAVQRLMESGMITVNG-MPPKPSLKLKGGEQLKIAVPPPVEAGP--APENIPLEILYEDRDLVVVNKGAGMVVHPGAGNSGGTLVNALLGHCTDLSGI---GGELRPGIVHRIDKDTSGILVVAKNDASHLALSEQFREHSIKRIYIAIVYGSPKTDSGRLESIIGRHPVDRKRMSGKARHGKHAVTHWRVIGRYPGMCLIRLRLETGRTHQIRVHLSEAGHPLVGDEVYGGGARLDSVKDPVLRRLIRELGRQALHAKTLGFVHPSTKEYLEFDTDLPRDMATIVEHLEK 315
>gi|50085931|ref|YP_047441.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate synthase) (Uracil hydrolyase) [Acinetobacter sp. ADP1] >gi|49531907|emb|CAG69619.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate synthase) (Uracil hydrolyase) [Acinetobacter sp. ADP1] (350 aa)
Score = 315, Expect = 2.9e-27, Identities = 89/290 (30%), Positives = 166/290 (57%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIY---------GPKHINKTTK--YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QR+D + ++ ++  SR   K  +++  + VNG+++ KP  + +    + L  E  +E      P    ++IVYED+ IL++NKP  ++VHP + + S TL N + Y +  K ++ +    R G+VHR+DK T GL++VAK+L++  + +K   D+ + + Y  +++ ++      +D  IKR     R +++     +EA T +    ++++FT  + +L TGRTHQIRVH  +I + ++ DP+Y           + + +T +    Q L A KL  +HP TQ+E+      P++F + ++
  S:    50 QRIDQVAATVWNEFSREKLKQWMKDGHLLVNGEVV-KPKYRCEGNELLTLNVE--LEAQTTSQPENIPLDIVYEDQDILVINKPAGMVVHPGAGNPSGTLVNALLYHY-PKAVELS----RAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLADKSVYRIYDLVVYGNIIAGGT-IDEQIKR-HPVDRIKMAILPGGREAVTHYNVKERFQHFTRVQAQLETGRTHQIRVHFSYIGHGLVGDPVYMSRVRVPAGASERLGQTLRGFKRQALHASKLGLVHPRTQEEMMFEAPWPEDFTQLLE 341
>gi|119513315|ref|ZP_01632353.1| Pseudouridine synthase, RluD [Nodularia spumigena CCY9414] >gi|119462022|gb|EAW43021.1| Pseudouridine synthase, RluD [Nodularia spumigena CCY9414] (309 aa)
Score = 315, Expect = 3.0e-27, Identities = 89/285 (31%), Positives = 146/285 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID--AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           +RLD  +S    +LSRS  +  IE   V +N +I +     V     I L+    + E + L    +DI  +I+YED ++LI+NKP  ++VHP       TL N +  +     +   G   R GIVHRLDK T G + +AK+  ++++       +   ++YL +++   +T   ++D PI R     ++     I+   + A T ++ + +  N TL   +L TGRTHQIRVH+  I + ++ DPIY   H       GQ L A++LK  HP ++  + +    P+ F
  S:    13 ERLDRYLSENLPNLSRSRIQQLIEQGNVHLNEQICTTKKITVKAGDRITLE----IPEVQPLQVQAQDIPLDILYEDDHLLILNKPAGLVVHPAPGHPDGTLVNAL--LAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYHSLQAQLQAKTARREYLGVVYGAPKTENGKIDEPIGRHPQDRKKMAVVPIEKGGRNAVTHWQILERLGNQTLVLFQLETGRTHQIRVHSAKIGHPIVGDPIYSSAHSVGVKLNGQALHAWRLKLQHPISENLIEVTAPPPQTF 296
>gi|157148106|ref|YP_001455425.1| 23S rRNA pseudouridine synthase D [Citrobacter koseri ATCC BAA-895] >gi|157085311|gb|ABV14989.1| hypothetical protein CKO_03916 [Citrobacter koseri ATCC BAA-895] (326 aa)
Score = 315, Expect = 3.1e-27, Identities = 99/289 (34%), Positives = 153/289 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I +  V VNGK+  KP  KV    ++ +  E  ++E     P    ++IVYED  IL++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  +S     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG     PK      I+   ++  Q L A  L+  HP +  E+  +  +P++  E I
  S:    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVSINAE--IDEEIRFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEAFISTLRQFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELI 309
>gi|150016471|ref|YP_001308725.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB 8052] >gi|149902936|gb|ABR33769.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB 8052] (305 aa)
Score = 315, Expect = 3.1e-27, Identities = 94/291 (32%), Positives = 156/291 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  ++  F   SRS  +  IE + + VN K   K N K+   +E E+   E +++       P    I I+YEDK +++VNKP  ++VHP   + + TL N +  ++  K +      +R GIVHR+DK T G+++VAK+ ++ N  +    D  ++++Y AL+   L+     +D P+ R     R ++      K A T ++ + ++  +TL +  L TGRTHQIRVH   I   ++ DP+YG K      K GQ L A  L F+HP   + +    ++P+ F+E I+K
  S:    15 ERIDKYLAEIFVDKSRSFIQGLIEKDDIKVNNKT-PKSNYKLRALDEIEVTFSEPEVLRVEAEEIP----INILYEDKDVVVVNKPQGMVVHPAPGNYNGTLVNAL--LYHCKDLSSINGIIRPGIVHRIDKDTSGVLVVAKNDEAHNKLSDQLKDHSMKREYYALVEGRLKNDKGIIDKPLAR-NKRDRLKIGIVEGGKRAVTHYEVLERFNGYTLIKCILETGRTHQIRVHMASIGFPLVGDPLYGFKKQRFKLK-GQVLHAKTLGFVHPSKNEYMEFTTELPEYFQEIIEK 299
>gi|186683943|ref|YP_001867139.1| RluA family pseudouridine synthase [Nostoc punctiforme PCC 73102] >gi|186466395|gb|ACC82196.1| pseudouridine synthase, RluA family [Nostoc punctiforme PCC 73102] (345 aa)
Score = 315, Expect = 3.1e-27, Identities = 87/289 (30%), Positives = 145/289 (50%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID--AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           R+D  +S +   LSRS  +  IE   V +N K+ +     V     I L+    + E + L    +DI  +I+YED  +LI+NKP  ++VHP       TL N +  +     +   G   R GIVHRLDK T G + +AK+  + +        +   ++YL +++   +  +  +D PI R     ++     I+   + A T ++ + +  NFTL   +L TGRTHQIRVH+  I + ++ DPIY   H       GQ L A++L+  HP + + + +    P +F + ++
  S:    50 RIDRFLSQELPDLSRSRIQQLIEQGNVQLNDKVCTSKKINVKLGDRITLE----IPEAQPLELLAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHPDGTLVNAL--LAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTEVAHHHLQAQLKAKTARREYLGVVYGAPKVESGTIDLPIGRHPQDRKKMAIMPIEQGGRSAVTHWQVLERLGNFTLIRFQLETGRTHQIRVHSAKIGHPIVGDPIYSSGHSVGVNLSGQALHAWRLRLQHPLSGEMIEVTATPPTQFTKLLE 337
>gi|183222495|ref|YP_001840491.1| pseudouridine synthase (Uracil hydrolyase) [Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'] >gi|189912533|ref|YP_001964088.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)'] >gi|167777209|gb|ABZ95510.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)'] >gi|167780917|gb|ABZ99215.1| Pseudouridine synthase (Uracil hydrolyase) [Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'] (312 aa)
Score = 315, Expect = 3.2e-27, Identities = 98/293 (33%), Positives = 150/293 (51%)
  Q:     3 NTQRLDILVSSKF--SLSRSIAKHKIENNLVTVNGK--IISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFK-----EINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFT-QKEVNINLDMPKEFKEYIKK 295
           +  RLD+ +       LSRS  +  I++  VT   K  ++ K   KV    E ++  + I      L P   DI ++Y++   ++++K   I  H    D S +L N + Y F  K +   G   R GIVHRLDK TEG++I+AK+  +  A +KLF D+ +EK Y A +          ++ PI R      +   R+ D + A T +K     +    + F+L ++ L TGRTHQIRVH   +   V+ D +Y  +     T+YG  L A KL F HPF   K + + LD P+ FK + +K
  S:    12 DQSRLDVFLKDNAGDDLSRSTVQKWIDSGFVTNKTKDQVVHKNGYKVALGEEFVV--DVIARPPSRLEPIAMDIPVLYDEDEFMVIHKKAGIACHSGPGDDSPSLVNGLLYQF--KNLSGTGGERRPGIVHRLDKPTEGVLIIAKTDRAHAALSKLFQDRLVEKTYYAWVLQAPVEAEGTINMPIGRHPVERVKMCVRE-DGRMAITHYKTEKIVQTQTGRKFSLMKLGLETGRTHQIRVHMAKVGCPVVGDSLYS-RSAKDYTQYGLLLFAKKLDFPHPFVPDKRIVVELDFPERFKVFERK 308
>gi|195953891|ref|YP_002122181.1| pseudouridine synthase, RluA family [Hydrogenobaculum sp. Y04AAS1] >gi|195933503|gb|ACG58203.1| pseudouridine synthase, RluA family [Hydrogenobaculum sp. Y04AAS1] (308 aa)
Score = 315, Expect = 3.4e-27, Identities = 100/290 (34%), Positives = 166/290 (57%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKD-------IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKH--INKTTKY--GQ--YLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R+D+L+S+ +  +SR   K  I+ N V +NG+ + K + KV E           V E ++  P K D       I+I+YED  + +V KP+ +  H       NTL N +   F    +   G   R GIVHRLD+ T GL+++AK+  S    + +F +++++K Y A+++   + +   ++  I+R  T+ R +     + K A T +      KN +L +++++TGRTHQIRVH  +I + ++ D +YG KH   +KT ++  G+   LVAYKL F+HP +QK +   +DMP  FK  +K
  S:    13 ERIDVLISNIYKDISREYIKRIIKENGVLINGEKVFKSSKKVFEND---------VLEFEIPPPKKLDVKAQDIHIDILYEDNDLAVVVKPSGMPSHTGPGHDENTLVNALLAKFGDLSVI--GGVERPGIVHRLDRYTHGLMVIAKNDVSHQKLSLMFKNKEVDKHYKAIVYGISRFKEQTIETFIRRHPTN-RLKFEVANEGKLAITKYSLEKPLKNASLLDIKIYTGRTHQIRVHMSYIGHPIVGDTLYGYKHSYFDKTLEHMIGKRFLLVAYKLSFLHPKSQKPMEFEIDMPDYFKNVLK 304
>gi|194289464|ref|YP_002005371.1| 23S rRNA pseudouridine synthase [Cupriavidus taiwanensis] >gi|193223299|emb|CAQ69304.1| 23S rRNA pseudouridine synthase [Cupriavidus taiwanensis] (418 aa)
Score = 314, Expect = 3.7e-27, Identities = 97/289 (33%), Positives = 158/289 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDP-----LRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVE---VDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKY---KNF-TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +RLD L++  FS  SRS  +  IE+  V V+G++  +P   V   + I ++ +    E     P    +++VYED  +L++NKP  ++VHP + + S T+ N +           + DP      R GIVHRLDK T GL++VA++L +     +    + +++ Y+AL+      RT +   +DAPI R     TR  + +    K +RT F+ +      + F ++   +L TGRTHQIRVH E I + ++ DP+Y      + T+ GQ                L AYKL  +HP T K ++     P++ +  I
  S:    75 ERLDKLLARHFSEFSRSRLQQWIESGAVRVDGQV-RRPRDAVQMGNRIEVQPQA-APEASAFAPEDVPLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGL----------LHRDPGAASLPRAGIVHRLDKETSGLMVVARTLTAQTDLVRQLQARTVKRTYIALVWG----RTYDEGTIDAPIGRDPRERTRMAIVQTASGKPSRTHFRTLATVPLGRGFVSMVMCKLETGRTHQIRVHFESIGHPLVGDPVY-----FRATQRGQRPAIRVPLPVPYERQALHAYKLGLVHPATGKHMSWTAQPPEDLQALI 371
>gi|171913853|ref|ZP_02929323.1| pseudouridine synthase, RluA family protein [Verrucomicrobium spinosum DSM 4136] (303 aa)
Score = 314, Expect = 4.0e-27, Identities = 90/293 (30%), Positives = 150/293 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDA-KEARTIFKEINKYKNFTLAEVELFTGRTHQIRVH-AEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           QRLD  +  +   +SR+  +  I++  + +NGK  +KPNT + +   I ++    V    V  P    + +++ED++I+++NKP+ ++VHP + +   TL N +  +F  K +   G  LR GIVHRLDK T G ++ AK   +    T+ F  + + K YLA ++    + +  ++  I R     +R      +A KEA T +  +  ++   L    L TGRTHQIRVH  E +   ++ D IY              L A+KL+F HP T+  +     +P+ F  ++KK G
  S:    13 QRLDHYLQGELPDMSRTRLQGLIKDGHILLNGKA-AKPNTPLKQGDRITMEVPDPVPTEVV--PQDIPLNVLFEDEHIIVINKPDGLVVHPAAGNPDGTLVNAL--LFHCKNLSGIGGELRPGIVHRLDKETSGCMVAAKHDLAHTRLTEAFSQRDLTKIYLAAVNGTPSSSSGRIENRIGRHPVDRKRMALVTGEAGKEALTEWDRVAVHQGCALIRCRLLTGRTHQIRVHMKEALGCPILGDTIYAQIQRQLIKMPRLMLHAWKLEFQHPITKLGLKFEAPVPEAFGPWMKKNG 303
>gi|123441245|ref|YP_001005232.1| 23S rRNA pseudouridine synthase D [Yersinia enterocolitica subsp. enterocolitica 8081] >gi|122088206|emb|CAL10994.1| ribosomal large subunit pseudouridine synthase D [Yersinia enterocolitica subsp. enterocolitica 8081] (325 aa)
Score = 314, Expect = 4.3e-27, Identities = 96/289 (33%), Positives = 155/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKY---------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I  + VTVNGK I+KP  KV    E++  + +I E+ +   P +  ++IVYED  IL++NKP  ++VHP + +   T+ N + Y +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   ++ T    VD PI R  ++ R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG  P+     +            Q L A  L+  HP +  ++  +  +P++  E I
  S:    18 QRLDQALAELFPDYSRSRIKEWILEDKVTVNGKTINKPKEKV-LGGELVAIDAQIEEDAR-WAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIM-----DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNM-TAGGRVDEPISR-HSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFIAILRGFDRQALHATMLRLYHPISGIQMEWHAALPEDMVELI 309
>gi|115379077|ref|ZP_01466202.1| ribosomal large subunit pseudouridine synthase D [Stigmatella aurantiaca DW4/3-1] >gi|115363904|gb|EAU63014.1| ribosomal large subunit pseudouridine synthase D [Stigmatella aurantiaca DW4/3-1] (262 aa)
Score = 313, Expect = 5.5e-27, Identities = 78/223 (34%), Positives = 123/223 (55%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINK------TTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +E+++ED+ +++VNK   ++VHP +   S TL N +  +   K +   G  LR GIVHRLDK T G ++VAK+  +  A  K F  + +EK YLAL+H H +     ++    R     +R   +  + K A T+F+    ++   L EV+L TGRTHQIRVH     + ++ D +YG     K        + G Q L A++L F HP T K + +   +P++F   +K
  S:    32 LEVLHEDRDLVVVNKAAGMVVHPGAGHASGTLVNAL--LHRVKDLAGVGGELRPGIVHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLALVHGHPKAEG-RIETLYGRHPVHRQRFTGKVKEGKSAVTVFRTREFFEGAALVEVDLLTGRTHQIRVHLSESGHPLLCDALYGAGRKAKGQVAQAQERLGRQALHAWRLGFAHPRTGKALKLEAPLPEDFAASMK 258
>gi|113867448|ref|YP_725937.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16] >gi|113526224|emb|CAJ92569.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16] (396 aa)
Score = 313, Expect = 5.5e-27, Identities = 98/289 (33%), Positives = 158/289 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPL--RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVE---VDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKY---KNF-TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +RLD L++  FS  SRS  +  IE+  V V+G +  +P   V   + I ++ +    E+   +P    +++VYED  +L++NKP  ++VHP + + S T+ N + +       +  G  L  R GIVHRLDK T GL++VA+SL +     +    + +++ Y+AL+      RT +   +DAPI R     TR  V      K +RT F+ +      + F ++   +L TGRTHQIRVH E I + ++ DP Y      + T+ GQ                L AY+L  +HP T K ++     P++ +  I
  S:    56 ERLDKLLARHFSEFSRSRLQQWIESGAVRVDGHV-RRPRDAVQMGNRIEIQPQA-APESSAFSPEDVPLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLH-------RDPGAALLPRAGIVHRLDKETSGLMVVARSLTAQTDLVRQLQARTVKRTYIALVWG----RTYDEGTIDAPIGRDPRERTRMAVVHTASGKPSRTHFRTLATVPLGRGFVSMVMCKLETGRTHQIRVHFESIGHPLVGDPAY-----FRATQRGQRPAVRAPLPVPYERQALHAYQLGLVHPATGKRMSWTAQPPQDLQALI 352
>gi|196165786|ref|ZP_03126317.1| putative pseudouridylate synthase [Clostridium difficile QCD-23m63] (300 aa)
Score = 313, Expect = 5.6e-27, Identities = 100/277 (36%), Positives = 157/277 (56%)
  Q:    19 RSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RS++K K E + V VNG +  KP+ KV     I   E KI EE     P   +++I+Y+D  I++VNK   ++VHPT      T+AN I Y  D++K     + +++  V+RLD  T GLVIVAK+  + +  +    + K+EKKY+ ++   ++     +D PI R  E S +R +  D   + + T +K I + +N T+ EV L TGRTHQIRVH   I + +I D +YG   +++     Q L AY+L+F  P T++++    D+P++ KE I K
  S:    35 RSLSKMKREKS-VLVNG-VYKKPSLKVYSGDLI---EVKINEEKANFEPQDLNLQIIYDDFDIIMVNKLPFMVVHPTKSHYDKTIANGISYYIDNQK-----ENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTEDSIKRII--DERGQSSVTHYKVIERLENATVLEVSLETGRTHQIRVHMAHIGHGIIGDELYGC--VDEELINRQALHAYRLEFEQPRTKEKLKFKADIPEDIKELISK 298
>gi|15806790|ref|NP_295512.1| ribosomal large subunit pseudouridine synthase D [Deinococcus radiodurans R1] >gi|6459564|gb|AAF11343.1|AE002020_2 ribosomal large subunit pseudouridine synthase D [Deinococcus radiodurans R1] (338 aa)
Score = 313, Expect = 5.8e-27, Identities = 86/284 (30%), Positives = 154/284 (54%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNG-DPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQT-RTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY-----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG------PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           RLD +VS    +SRS     IE  LV ++G+  SK + K+     + +    +   +  + P    +++++ED++++ +NKP  ++ HP    +S TL N ++  +   ++  ++G D  R GIVHRLDK T G+++VAK++ +       F D++ +K YLA+     +  R V+VDAPI R +   +R       A+EA+T+F  ++ +     +   L   +  TGRTHQIRVH   + + ++ D +YG      P+H          L A  L+  HP +   +++   +P++ 
  S:    32 RLDAVVSLLSGVSRSQVAGWIEAGLVEIDGRAASKASQKLRGGEALRVSPPPL--PSAQVEPEDVPLDVIFEDEHLIAINKPPGMVTHPAPGVISGTLVNALLGRMSLPEQQDFDGPDGYRPGIVHRLDKDTSGVIVVAKTVAAHARLAAAFKDRETKKTYLAIAAGAWKAERPVQVDAPIGRHQIQRQRMTVGGAGAREAQTLFTPLDAHPDGHGRTLALVRAQPRTGRTHQIRVHLAHLGSPILGDAVYGRASEIMPRHA---------LHAQFLEVPHPVSGDILHLQAAVPEDL 318
>gi|86605450|ref|YP_474213.1| RluA family pseudouridine synthase [Synechococcus sp. JA-3-3Ab] >gi|86553992|gb|ABC98950.1| pseudouridine synthase, RluA family [Synechococcus sp. JA-3-3Ab] (310 aa)
Score = 312, Expect = 6.0e-27, Identities = 85/290 (29%), Positives = 145/290 (50%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKV-LTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRR-EVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           RLD  ++ +   LSRS  +  I    V +NG+     +  +    +I   E +I   T   L P +  ++I+YED+ +L++NKP  ++VHP     S TL + +  +    ++       R GIVHRLDK T G +++AK   +          +   + YL ++          + API R     ++  V      + A T ++ + +  N+TL + EL TGRTHQIRVHA  ++  ++ DP+Y     +     GQ L A+KL F+HP T + + +   +P+EF+  +++
  S:    17 RLDRGLAEQLPELSRSRLQQLIRQGQVWLNGQPCLDKDRPLQAGDQI---EVRIPPATPTPLQPERIPLDILYEDEDLLVINKPRGLVVHPAPGHASGTLVHAL--LAHCPRLSGINGEQRPGIVHRLDKDTTGALVIAKHDQAHQHLQAQIQAKTARRIYLGVVFGRPAQSQGTISAPIGRHPVDRQKMAVVPPGQGRAAVTHWQVLERLGNYTLMQFELETGRTHQIRVHAAHLRLPIVGDPLYTQSKTSPVKLSGQALHAWKLSFVHPRTGQPLQVTAPLPEEFERLLRQ 304
>gi|160935585|ref|ZP_02082960.1| hypothetical protein CLOBOL_00475 [Clostridium bolteae ATCC BAA-613] >gi|158441329|gb|EDP19039.1| hypothetical protein CLOBOL_00475 [Clostridium bolteae ATCC BAA-613] (287 aa)
Score = 312, Expect = 6.4e-27, Identities = 83/250 (33%), Positives = 140/250 (56%)
  Q:    44 KVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEI--NKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP--KHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           K  +  E+ L EE   E++  + P K  + IVYED+ IL++NK   + +HP+     NTLAN + + F  K     G+     +++RLD+ T GL+++A+ + S    ++    ++I ++Y A++  H       VD+PI R E ST   + R +D    + A T F+ +  N+ K+ +L  + L TGRTHQIRVH   I + +  D +Y P  ++I++     Q L +Y L+F HP T KE+     +P++ K+ +
  S:    44 KTGQTVEVTLPEE---EDSGNIVPVKLPLSIVYEDEDILVINKDAGVPIHPSQGHYDNTLANAVSWYFHEK-----GEAFTYRVINRLDRDTTGLLVLARHMLSACILSEQMTGRRIRREYRAIVLGHTPEEGT-VDSPIARAEGST---IERRVDHETGERAVTHFRTLLYNEEKDLSLVSLSLETGRTHQIRVHMRSIGHPLPGDFLYCPDYRYIDR-----QPLHSYLLRFEHPITGKEMEFTAGLPEDMKQLL 283
>gi|183597510|ref|ZP_02959003.1| hypothetical protein PROSTU_00783 [Providencia stuartii ATCC 25827] >gi|188023155|gb|EDU61195.1| hypothetical protein PROSTU_00783 [Providencia stuartii ATCC 25827] (325 aa)
Score = 312, Expect = 6.5e-27, Identities = 95/290 (32%), Positives = 157/290 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKY---------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I ++ V VNGK+I+KP  KV    +I++  + ++EE     P    +++VYED+ IL++NKP  ++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+    + T    V+ PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + +I DP+YG  P+ +   ++           Q L A  L+  HP +  ++  +  +P +  E I+
  S:    18 QRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKPKEKVLGGEQILV--DALIEEDNRWEPQDIPLDVVYEDEDILVINKPRGLVVHPGAGNPDGTILNALLHRYPEIV-----DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAVGRM-TAGGMVEEPISRHPTK-RTHMAVHPMGKPAITHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLIGDPLYGGRPRPLKGASEEFFEVMRKFDRQALHATMLRLYHPISGIQMEWHAPLPDDMVELIE 310
>gi|88811115|ref|ZP_01126371.1| ribosomal large subunit pseudouridine synthase D [Nitrococcus mobilis Nb-231] >gi|88791654|gb|EAR22765.1| ribosomal large subunit pseudouridine synthase D [Nitrococcus mobilis Nb-231] (315 aa)
Score = 312, Expect = 6.8e-27, Identities = 91/285 (31%), Positives = 152/285 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEES---EIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           QR D  +++ F   SRS  +  +++  +TV+  ++   +     E     ++L+EE  V    +       + IVYED  +L+++KP  +IVHP +     TL N + + +D +     G P R GIVHRLDK T GL++VA++L +     +    + +++ YLAL+ + + T      A I R      R   R  D + A T F+ + ++   TL    L TGRTHQIRVH  +++  V+ DP+YG     PK  ++  K        Q L A +L+ +HP T++ V  +  +P ++
  S:    18 QRFDRALATIFPQYSRSRLQAWLKSGAITVDTTVLRAKDLVCGGEQVRLSVLLEEEGAVAAEPIA------LRIVYEDDSLLVIDKPPSLIVHPGAGHAGGTLQNALLH-YDPR---LAGLP-RAGIVHRLDKGTSGLMVVARNLTAHKLLVEQLQARSVKRDYLALV-SAVVTSGGRATAAIGRHRRDRTRMAVRQ-DGRAAVTHFRVVERFAAHTLLRCSLETGRTHQIRVHMAWLRQPVVGDPVYGGRTRLPKGASEELKTALSGFRRQALHALELRLVHPATEQAVGWHSPLPADY 304
>gi|87119407|ref|ZP_01075304.1| ribosomal large subunit pseudouridine synthase D [Marinomonas sp. MED121] >gi|86164883|gb|EAQ66151.1| ribosomal large subunit pseudouridine synthase D [Marinomonas sp. MED121] (322 aa)
Score = 312, Expect = 6.9e-27, Identities = 95/292 (32%), Positives = 158/292 (54%)
  Q:     3 NTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEI--ILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           N QR D++ +  FS  SRS  +  I+  ++ V+GK      +K  E+  +  ++  E +VE+     P    ++IVYED+ IL+VNKP+ ++VHP     S TL N I +         +    R GIVHRLDK T GL++VAK+L +         D+ + ++Y A+    + T    V+ PI R   + ++     ++ K+A T ++ + ++KN T   ++L TGRTHQIRVH   I+  ++ DP Y           P+  ++   +  Q L A +L+  HP T + +   +D+P + K  I+
  S:    16 NGQRFDLIATELFSDYSRSRIQAWIKEGVLLVDGK-----KSKAKEKLFVGEVISLETLVEDIDDHQPEDIPLDIVYEDEDILVVNKPSGLVVHPAVGHRSGTLMNAILF-----HCPESAHVPRAGIVHRLDKETTGLMVVAKTLAAQTELVSQLQDRSMGREYEAVAIG-IMTGGGTVNEPIGRHPQNRQKMAVEPLNGKDAVTHYRLLQRFKNHTHIRLKLETGRTHQIRVHMSHIQFPLLGDPQYAGRMKMPKACIPELRDELQNFRRQALHAKRLELSHPITGEFMEWEVDLPDDMKHLIE 310
>gi|89055892|ref|YP_511343.1| ribosomal large subunit pseudouridine synthase D [Jannaschia sp. CCS1] >gi|88865441|gb|ABD56318.1| ribosomal large subunit pseudouridine synthase D [Jannaschia sp. CCS1] (310 aa)
Score = 312, Expect = 7.2e-27, Identities = 87/261 (33%), Positives = 135/261 (51%)
  Q:    16 SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEES--EIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHN---------------HLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---------QYLVAYKLKFIHPFTQ 276
           ++SR+     I    V +NG++++ P  +V E    EI +++   VE      P    ++IV+ED  +++VNKP  ++VHP     S TL N + + F  K     G+  R GIVHR+DK T GL++VAKS  + +     F D  +E++YLAL H                  +  TV++   + R +T  +R+       + A T  + +  +    L    L TGRTHQIRVH   + + +I D  YG +        G         Q L A  L F+HP +Q
  S:     6 AISRTRLARLIPAGAVAINGRVVTDPKARVAEGDGVEITVEDAAEVETVAEDIP----LDIVHEDDDLIVVNKPAGMVVHPAPGSPSGTLVNALLHHFGGKLSGVGGEK-RPGIVHRIDKDTSGLLVVAKSDRAHHGLAAQFADHSMEREYLALCHGVPDGSDPRLRGVKGVSFEGSTVKITTQLARHKTDRQRQAVLFSGGRHAVTRVRVLEAHGPVALVSCRLETGRTHQIRVHMSHVGHALIGDQTYGGRRKISAKLPGAEAVNAFPRQALHAATLGFVHPVSQ 287
>gi|67920300|ref|ZP_00513820.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501] >gi|67857784|gb|EAM53023.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501] (313 aa)
Score = 312, Expect = 7.2e-27, Identities = 89/284 (31%), Positives = 155/284 (54%)
  Q:     6 RLDILVSSKFS-LSRSIAKHKIENNLVTVNGKII--SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVE-------VDAPIKRVETSTRRE--VSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           RLDI +S++ + +SRS  +  IE   +T+N ++    K   K+ +  ++ + E + +E    L P    ++I+YED+ ++I+NK  +++VHP     + TL + +  ++    +   G   R GIVHRLDK T G ++VAK+  +         ++  +++YL +++  L     E       ++ PI R     +R   V R+   +EA T ++ I +  N++L +  L TGRTHQIRVH+ +  N ++ DP+Y      K    GQ L A+KL   HP T +++     +P EF
  S:    13 RLDIWLSNQLTDISRSRIQKLIEQGNITLNNEVCPNKKIKLKIGDRLQVNIPEPQPLE----LQPEPIPLDILYEDEQLIIINKSANLVVHPAPGHETGTLVHAL--LYHCSNLAGIGGVQRPGIVHRLDKDTTGAIVVAKTDFAHQNLQFQIKNRTAKREYLGIIYGVLNNEEDENNRDKGMINLPIGRHPVDRKRMAVVPREKPGREAVTYWEIIERLGNYSLVKFILETGRTHQIRVHSSYFGNPIVGDPLYSNNRSLKMNLSGQALHAHKLTLTHPITSEKIEAIAPLPDEF 302
>gi|157737249|ref|YP_001489932.1| ribosomal large subunit pseudouridine synthase D [Arcobacter butzleri RM4018] >gi|157699103|gb|ABV67263.1| ribosomal large subunit pseudouridine synthase D [Arcobacter butzleri RM4018] (328 aa)
Score = 312, Expect = 7.5e-27, Identities = 96/290 (33%), Positives = 161/290 (55%)
  Q:     4 TQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEES--EIILKEEKIV----EETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN--FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK-HINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           T RLD  ++     SR+  +  I+   V V+GKI +K   K+ E    E+   E ++     EE    +   K++EI+YED YIL++NKP ++ VH        TL + +K    +  +       R GIVHRLDK T G++++AK+ ++    +K   D+ + + YLA+L   L+   + ++ PI+R   + R ++S + + + A++ F +I    N  F L   +L+TGRTHQIRVH   I  H++ D +YG K  +NK  ++   L AY L   HP T K++    ++P++ K ++
  S:    10 TNRLDKFLAQNIDASRNQIEQLIKKEFVKVDGKITNKTGLKLKENQNVEVFFPETQLNKRKDEEFLKNSLEDKEVEIIYEDDYILVLNKPYNLTVHDAPSVKDATLVDWLK--LKNISLSTISGEERHGIVHRLDKGTSGVMVIAKTNEAHLNLSKQLEDKSMGRYYLAILDLALKENVI-IEKPIRR-NPNNRLKMSIEENGRYAKSAFSKIALSDNEKFELIACKLYTGRTHQIRVHLSSINRHILGDNLYGFKGELNKINRF--LLHAYYLYLTHPVTNKQMCFKANLPEDMKNFL 302
>gi|148978562|ref|ZP_01815014.1| 23S rRNA pseudouridine synthase D [Vibrionales bacterium SWAT-3] >gi|145962351|gb|EDK27632.1| 23S rRNA pseudouridine synthase D [Vibrionales bacterium SWAT-3] (324 aa)
Score = 311, Expect = 7.9e-27, Identities = 95/284 (33%), Positives = 157/284 (55%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKT-TKY-----GQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  V+  F+  SRS  K  + +  V V+G++I+KP  KV    EIIL+ E  +E+ +        ++IV+ED+++L++NKP D +VHP +     T+ N + + +         +  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+    + T    V+  I R   + R  ++ +   K A T ++    ++  T   + L TGRTHQIRVH  ++++ ++ D  YG     PK  ++  TK       Q L A  LKF+HP T +EV  +  +P +
  S:    18 QRLDQAVAELFTDFSRSRIKEWLLDGKVQVDGEVITKPRVKVMGGEEIILQAE--LEDEERWEAQDIPLDIVFEDEHLLVINKPRDFVVHPGAGTPDGTVLNALLHHYPQI-----AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKM-TAGGMVEKGISR-HATKRTLMAVNETGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPKGASEELTKMIRAFDRQALHAVMLKFVHPITGEEVEFHAPVPND 304
>gi|169195601|ref|ZP_02854973.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv. trifolii WSM2304] >gi|169092193|gb|EDS70902.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv. trifolii WSM2304] (341 aa)
Score = 311, Expect = 8.2e-27, Identities = 100/289 (34%), Positives = 165/289 (57%)
  Q:     6 RLDILVSSKF--SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPL-------RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQ----KIEKKYLALLHNHLQTRTVEVDAPIKRVETS-TRREVSR--DIDAKEARTIFKEINKYKN-------FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTK--YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD  ++++     SRS  K  I++  V++ G+ ++ P  KV          E  + E +  TP  +DI  +I++ED+ +++++KP+ ++VHP S + + TL N +        I + GD L       R GIVHRLDK T G+++VAK+  +    +  F D      +E+ Y A++    ++ T  VDAP+ R     TRR V R    DA EA T ++ I +++         +L E  L TGRTHQIRVH   I + ++ D +YG          P+ + K       Q L A+ L+F HP T + ++  + +P +  E ++
  S:    24 RLDAWLTAQVGEEFSRSRIKALIKDGQVSLRGEPVTDPQRKVRNGDSF----EITLPEPEDPTPQGEDIPLDILHEDEDLIVISKPSGLVVHPGSGNWTGTLVNAL--------IHHCGDTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTMPLERAYQAVVWGRPRSLTGTVDAPLGRATGDRTRRAVKRPDSHDADEAITHYEVIERFQENPDATALASLVECHLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANRLPEEVRKVVNGFNRQALHAFMLQFEHPRTGELMHFEVPLPDDMVELVE 337
>gi|156740304|ref|YP_001430433.1| RluA family pseudouridine synthase [Roseiflexus castenholzii DSM 13941] >gi|156231632|gb|ABU56415.1| pseudouridine synthase, RluA family [Roseiflexus castenholzii DSM 13941] (315 aa)
Score = 311, Expect = 8.4e-27, Identities = 91/285 (31%), Positives = 148/285 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPN-TKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
            RLD  ++ K   LSR+ A+H IE+  V +N + +   +  +V +   + L E + V       P    ++IVYED  +++++KP  I+VHP       TL N +  I    ++  +GD LR GIVHRLD+ T GL++ A++  + ++       +++ K YL ++   +      +DAPI R  T  R  ++     + ART ++ + +   + L E  L TGRTHQIRVH       V+ DP+YGPK    T  +G   Q+L A++L F  P +   V     +P + 
  S:    18 HRLDRYIAGKVPDLSRTYARHLIEDARVLLNNRQVRPASPVRVGDVVTVQLPEPQPVGLVAEALP----LQIVYEDDDVVVIDKPAGIVVHPAPGHNRGTLVNAL--IARYPEMAISGD-LRPGIVHRLDRDTSGLLVAARNDRALHSLQAQQQARRMLKIYLVVVEGRMNESGGVIDAPIARHPTD-RVRMAVMAGGRPARTHWRVLEELGEYALIEARLETGRTHQIRVHFASRNRPVLADPLYGPKRPRAT--FGLTRQFLHAHRLGFALPSSGAWVEFTSPLPDDL 297
>gi|77956724|ref|ZP_00820806.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Yersinia bercovieri ATCC 43970] (325 aa)
Score = 311, Expect = 8.5e-27, Identities = 97/289 (33%), Positives = 157/289 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINK---TTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I  + VTV+GK I+KP  KV    E++  + +I E+ +   P +  ++IVYED  IL++NKP  ++VHP + +   T+ N + Y +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   ++ T    VD PI R  ++ R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG     P+  +    T   G   Q L A  L+  HP +  ++  +  +P++  E I
  S:    18 QRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKV-LGGELVTIDAQIEEDAR-WAPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIV-----DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNM-TAGGRVDEPISR-HSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFITILRGFDRQALHATMLRLYHPISGIQMEWHAALPEDMVELI 309
>gi|153953520|ref|YP_001394285.1| RluD1 [Clostridium kluyveri DSM 555] >gi|146346401|gb|EDK32937.1| RluD1 [Clostridium kluyveri DSM 555] (299 aa)
Score = 311, Expect = 9.2e-27, Identities = 86/238 (36%), Positives = 136/238 (57%)
  Q:    58 IVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTI--FKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           I EE++ +   K DIE+VYED+ I++VNK   I+VHPT    S TLAN + Y F       +G+   + +V RLD  T GL+IVAK+  +    ++    +  EK Y+A++H  ++     +D PI R E     ++ R +D +  R+I  +K I ++K+  L ++ L TGRTHQIRVH  ++ + +  D +YG +  N+     Q L AY+LKF HP   K + +  D+P++    IK+
  S:    67 IKEESQNIGAEKMDIEVVYEDRDIIVVNKKPGIVVHPTRSYPSGTLANGLIYYFQK-----SGENCIVRLVSRLDMDTSGLIIVAKNQFAHMCLSRDMKSEDFEKSYIAVIHGKMKEGQGIIDLPIYRPEGD---DIRRIVDKRGQRSITHYKVIEEFKHDQLLKLILKTGRTHQIRVHLSYLGHPLYGDTLYGIEGDNRYINR-QALHAYRLKFPHPRGNKILELETDIPEDISHLIKE 297
>gi|145628474|ref|ZP_01784274.1| SfhB [Haemophilus influenzae 22.1-21] >gi|144978944|gb|EDJ88630.1| SfhB [Haemophilus influenzae 22.1-21] (324 aa)
Score = 311, Expect = 9.8e-27, Identities = 99/289 (34%), Positives = 156/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYGQYLVAYK--------LKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  IE +LV +N +I + P  KV   E  EII++    VE+     P    + IVYED  I+++NKP D++VHP + + + T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+   VD P+ R   + R  ++     K A T ++ +  Y+N+T   + L TGRTHQIRVH   I + ++ D  YG     PK  N +  + + L  +K        L+  HP T + +     +P +F E +
  S:    17 QRLDQTLAELFPEYSRSRLKTWIEADLVNLNDRIANIPREKVFGGERIEIIVE----VEDDTRFEPENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI-----AEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASG-IMTKGGTVDQPMAR-HATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPK--NASEDFMEVLRNFKRQALHAVMLRLSHPITGEMMEWYAPLPDDFVELL 308
>gi|149371695|ref|ZP_01891111.1| ribosomal large subunit pseudouridine synthase D [unidentified eubacterium SCB49] >gi|149355322|gb|EDM43882.1| ribosomal large subunit pseudouridine synthase D [unidentified eubacterium SCB49] (348 aa)
Score = 311, Expect = 9.9e-27, Identities = 86/233 (36%), Positives = 137/233 (58%)
  Q:    64 VLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKE----ARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           +LTP   DI+IVYED  +L+VNK   ++VHP   + S TL N + +  D+     N    R G+VHR+DK T GL++VAK+ ++     K F D+  E++Y+AL+  +++     ++  I R  +   +  V  D DA+E    A T FK + ++   TL   +L TGRTHQIRVH +FI + + ND  YG + I K T + +Y               L A  L F+HP T + +     +P++ ++ ++K+
  S:    90 LLTPEDIDIDIVYEDDDLLVVNKQPGMVVHPGHGNYSGTLINALIHHIDNLP---NNSSNRPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTTEREYVALVWGNIEDDEGTIEGHIGRHPKNRLQNTVFLDEDAEEKGKAAVTHFKVLERFGYVTLVSCKLETGRTHQIRVHMKFIGHTLFNDERYGGEKILKGTTFSKYKQFVDNCFKVLPRQALHARTLGFVHPTTGEMMRFESKVPQDIEDCLEKW 339
>gi|28897333|ref|NP_796938.1| 23S rRNA pseudouridine synthase D [Vibrio parahaemolyticus RIMD 2210633] >gi|153839761|ref|ZP_01992428.1| ribosomal large subunit pseudouridine synthase D [Vibrio parahaemolyticus AQ3810] >gi|34395767|sp|Q87S65|RLUD_VIBPA Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|28805542|dbj|BAC58822.1| ribosomal large subunit pseudouridine synthase D [Vibrio parahaemolyticus RIMD 2210633] >gi|149746714|gb|EDM57702.1| ribosomal large subunit pseudouridine synthase D [Vibrio parahaemolyticus AQ3810] (325 aa)
Score = 310, Expect = 1.0e-26, Identities = 93/284 (32%), Positives = 153/284 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG-----------QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  ++  F+  SRS  K  + +  V VNG++++KP TKV    EI L+ E  +E+ +        ++IVYED  I+++NKP D +VHP +     T+ N + + + D  ++       R GIVHRLDK T GL++VAK++ +     +    + I ++Y A+    + T   +VD PI R  ++ R  ++     K A T ++    ++  T   + L TGRTHQIRVH  ++++ ++ D  YG +    T               Q L A  L+F HP T +E+  +  +P +
  S:    18 QRLDQAIAELFADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEITLQAE--LEDEERWEAQDIPLDIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAEVP------RAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRM-TAGGKVDQPIGR-HSTKRTLMAVAPLGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASQELTDMIRGFDRQALHAVMLRFEHPITGEELEFHAPVPDD 304
>gi|56460291|ref|YP_155572.1| 23S rRNA pseudouridine synthase D [Idiomarina loihiensis L2TR] >gi|56179301|gb|AAV82023.1| Pseudouridylate synthase [Idiomarina loihiensis L2TR] (322 aa)
Score = 310, Expect = 1.1e-26, Identities = 101/291 (34%), Positives = 154/291 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPL-----RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINK---TTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +RLD  ++  F   SRS  K  I +  VT++ K+I KP  KV   + + +  E   EE     P   +++IVYED  IL++NKP  ++VHP +     TL N ++ Y           DP      R GI+HRLDK T GL++VA+++ +      +  D+ I ++Y A+  N + T    VD PI R  T  R  ++     K A T ++ +++Y+  TL  + L +GRTHQIRVH   I++ ++ D  YG     PK        T  G   Q L A  L   HP T   +  N+  P +F+  I++
  S:    18 KRLDQALAELFPDYSRSRLKSWITDGKVTIDTKVIEKPREKVVAGALVAVDAEIEGEERHAAQP--VELDIVYEDDDILVINKPAGLVVHPGAGAPDRTLLNGLLHY-----------DPQLDLVPRAGIIHRLDKDTTGLMVVARNVPAQTQLVSMMQDRDITREYEAVC-NGVMTAGGMVDQPIGRHPTK-RTHMAVVQSGKPAVTHYRVLDRYRAHTLLRLRLESGRTHQIRVHMAHIRHPLVGDLTYGGRPRPPKQAEDRLLQTLRGFNRQALHAASLGLHHPITGDWLEFNVPRPTDFQYLIEE 311
>gi|77960425|ref|ZP_00824296.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Yersinia mollaretii ATCC 43969] (325 aa)
Score = 310, Expect = 1.1e-26, Identities = 95/289 (32%), Positives = 155/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKY---------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I  + VTV+GK I+KP  KV    E++  + +I E+ +   P +  ++IVYED  IL++NKP  ++VHP + +   T+ N + Y +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   ++ T    VD PI R  ++ R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG  P+     +            Q L A  L+  HP +  ++  +  +P++  E I
  S:    18 QRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKV-LGGELVAIDAQIEEDAR-WAPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIV-----DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNM-TAGGRVDEPISR-HSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFIAILRGFDRQALHATMLRLYHPISGIQMEWHAALPEDMVELI 309
>gi|168187890|ref|ZP_02622525.1| hypothetical RNA pseudouridine synthase YhcT [Clostridium botulinum C str. Eklund] >gi|169294254|gb|EDS76387.1| hypothetical RNA pseudouridine synthase YhcT [Clostridium botulinum C str. Eklund] (301 aa)
Score = 310, Expect = 1.1e-26, Identities = 87/239 (36%), Positives = 136/239 (56%)
  Q:    60 EETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           +E + + P K  ++I+YED+ I+++NKP  I+VHPT   L+ TL+N + Y F  K    N + + + +V+RLD  T GLV++AK+  S  A ++        K+YLA++H +L+ ++  +D PI RV   T + V  D   +++ T FK I  Y+N  L E+ L TGRTHQIRVH   I + +  D +YG +      +  Q L AYKL+  HP   + + +  D+P + K  I K  K
  S:    71 KEEQDIVPEKMKLDIIYEDEDIIVINKPKAIVVHPTKRHLNGTLSNGVLYYFKEK----NENSI-VRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFIKRYLAIVHGNLEEKSGVIDKPIYRVGEGTLKRVI-DERGQKSITRFKVIESYENADLIELTLETGRTHQIRVHLSSIGHPIYGDALYGKEEHEYIDR--QALHAYKLQIPHPKDGRILKLQSDLPDDMKNLIDKLKK 301
>gi|27363948|ref|NP_759476.1| 23S rRNA pseudouridine synthase D [Vibrio vulnificus CMCP6] >gi|34395776|sp|Q8DEV0|RLUD_VIBVU Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|27360065|gb|AAO09003.1|AE016798_163 Pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus CMCP6] (325 aa)
Score = 310, Expect = 1.2e-26, Identities = 97/287 (33%), Positives = 157/287 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWK-KDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKY------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           QRLD  ++  F+  SRS  K  + +  VTV+G +++KP TKV    E+I    ++ +E +    W+ +DI  +IVYED  IL++NKP D +VHP +     T+ N +  +F   ++    +  R GIVHRLDK T GL++VAK++ +     +    + I ++Y A+    + T   +VD PI R   + R  ++     K A T F+    ++  T   + L TGRTHQIRVH  ++++ ++ D  YG     P   ++           Q L A  L+F HP T +E+  +  +P +  E
  S:    18 QRLDQAIAELFADFSRSRLKEWLLDGKVTVDGNVVTKPRTKV-MGGEVITVLAELEDEVR----WEAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNAL--LFHCPEV---AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRM-TAGGKVDKPIGR-HATKRTLMAVSPMGKPAVTHFRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDAAYGGRARIPAGASEDVTAMIRNFDRQALHAVMLRFEHPITGEEMEFHAPVPDDMVE 307
>gi|72161527|ref|YP_289184.1| ribosomal large subunit pseudouridine synthase D [Thermobifida fusca YX] >gi|71915259|gb|AAZ55161.1| ribosomal large subunit pseudouridine synthase D [Thermobifida fusca YX] (309 aa)
Score = 310, Expect = 1.2e-26, Identities = 84/289 (29%), Positives = 144/289 (49%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD  ++  F LSR+ A   I    V V+G   +K + +V+  + + +                  + IVYED  I++V+KP  ++ HPT      T+ + +  +     +  +G   R GIVHRLD  T GL++VAKS  ++++  + F ++ +EK Y AL+  H       +DAPI R  +   R  +     + + T +  +  ++  +L E++L TGRTHQIRVH   I++  + D +YG  P    +   + Q+L A +L F HP   + V      P++  + ++
  S:    17 RLDTAIARLFGLSRTRAAELIAEGNVLVDGAPAAKSD-RVNAGAWLDITLPPPPNPPAPRPEPVPGMRIVYEDADIVVVDKPAGVVAHPTIGWSGPTVVDGL--LAAGVAVATSGAAERQGIVHRLDANTTGLMVVAKSEIAYSSLKRAFKERTVEKVYHALVQGHPDPLRGTIDAPIDRHPSGDGR-FAVVAGGRPSVTHYTTLEAFRAASLLEIDLETGRTHQIRVHMSAIRHPCVGDTLYGADPTLAERLGVHRQWLHAIRLAFTHPTQYRRVEFTSSYPEDLAKSLE 303
>gi|110800540|ref|YP_696800.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC 13124] >gi|168208824|ref|ZP_02634449.1| pseudouridine synthase, RluA family [Clostridium perfringens B str. ATCC 3626] >gi|110675187|gb|ABG84174.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC 13124] >gi|170713119|gb|EDT25301.1| pseudouridine synthase, RluA family [Clostridium perfringens B str. ATCC 3626] (298 aa)
Score = 309, Expect = 1.3e-26, Identities = 96/293 (32%), Positives = 154/293 (52%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + +++   +  +  LS  + +    +  + V+G +  K N  V    EI ++  K  +E++ + P K DIEIVYED  IL++NK   ++VHPT    + TLAN I Y F     K +     + +V RLD  T GL+I+ K+  +    +      K +K+YLA++H +L+ +   ++ PI R    T + V  D   +E+ T +K I  YK   L E  L TGRTHQIRVH   + + +  D +YG +     ++  Q L AY L F  P T+K +++  D+P++ KE I K
  S:    13 DKRKIREFLKEELGLSSRLIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSK--KESQNIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYF-----KESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-DERGQESITHYKVIESYKGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISR--QALHAYGLDFYSPKTKKPLSLRADLPEDMKELINK 294
>gi|77976239|ref|ZP_00831748.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Yersinia intermedia ATCC 29909] (325 aa)
Score = 309, Expect = 1.3e-26, Identities = 95/289 (32%), Positives = 154/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKY---------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I  + VTV+GK I+KP  KV    E++  + +I E+ +   P    ++IVYED  IL++NKP  ++VHP + +   T+ N + Y +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   ++ T    VD PI R  ++ R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG  P+     +            Q L A  L+  HP +  ++  +  +P++  E I
  S:    18 QRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKV-LGGELVAIDAQIEEDAR-WAPQDIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTILNALLYYYPEIM-----DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNM-TAGGRVDEPISR-HSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFISILRGFDRQALHATMLRLYHPISGIQMEWHAALPEDMVELI 309
>gi|25028588|ref|NP_738642.1| putative ribosomal large subunit pseudouridine synthase [Corynebacterium efficiens YS-314] >gi|23493873|dbj|BAC18842.1| putative ribosomal large subunit pseudouridine synthase [Corynebacterium efficiens YS-314] (309 aa)
Score = 309, Expect = 1.3e-26, Identities = 88/285 (30%), Positives = 143/285 (50%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKV-DEESEIILKE--EKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPT-SYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           R+D  +S    +SR+ A    E   V+V+G  + K +  V D   +++L E  + +V   +++      ++I+Y D  ++ VNKP  +  HPT  ++    +  +    F   +I  +G P R GIV RLD  T G+++VA S   +    + F D+ ++K Y AL+  H       ++API R  +S  R  +   D K A T ++ I  ++  TL +V L TGRTHQIRVH   + +    DP+YG  P    +     Q+L A  L F HP   + + I    P + +
  S:    18 RVDAALSKLLGISRTTAAELAEAGDVSVDGSAVRKSDRLVADSMLDVLLPEPAQPLVPREEIV----PGLDILYADDDLIAVNKPVGVAAHPTVGWEGPTVVGGLAAAGF---RISTSGPPERKGIVQRLDVGTSGVMVVAASERGYTVLKRAFRDRTVQKTYHALVQGHPDPTEGTIEAPIGRHPSSGWR-FAVTTDGKHAVTHYETIEAFQEATLVKVHLETGRTHQIRVHFSALHHPCCGDPMYGSDPALSERLGLIRQWLHAVSLGFHHPADGRWMEITSPYPDDLQ 300
>gi|37678897|ref|NP_933506.1| 23S rRNA pseudouridine synthase D [Vibrio vulnificus YJ016] >gi|37197638|dbj|BAC93477.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus YJ016] (325 aa)
Score = 309, Expect = 1.4e-26, Identities = 97/287 (33%), Positives = 157/287 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWK-KDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKY------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           QRLD  ++  F+  SRS  K  + +  VTV+G +++KP TKV    E+I    ++ +E +    W+ +DI  +IVYED  IL++NKP D +VHP +     T+ N +  +F   ++    +  R GIVHRLDK T GL++VAK++ +     +    + I ++Y A+    + T   +VD PI R   + R  ++     K A T F+    ++  T   + L TGRTHQIRVH  ++++ ++ D  YG     P   ++           Q L A  L+F HP T +E+  +  +P +  E
  S:    18 QRLDQAIAELFADFSRSRLKEWLLDGKVTVDGNVVTKPRTKV-MGGEVITVLAELEDEVR----WEAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNAL--LFHCPEV---AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRHITREYEAIAIGRM-TAGGKVDKPIGR-HATKRTLMAVSPMGKPAVTHFRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDAAYGGRARIPAGASEDVTAMIRNFDRQALHAVMLRFEHPITGEEMEFHAPVPDDMVE 307
>gi|33860753|ref|NP_892314.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus subsp. pastoris str. CCMP1986] >gi|33633695|emb|CAE18652.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus subsp. pastoris str. CCMP1986] (322 aa)
Score = 309, Expect = 1.4e-26, Identities = 94/294 (31%), Positives = 152/294 (51%)
  Q:     1 MKNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETST-RREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           M    RLD  LVS +   SR+  ++ I   LV VN K   +K   K  +  +I +      E    L P K ++ I++ED++I+++NK + +IVHP     S TL N +  +F  K +      LR GIVHRLDK T G ++VAKS +S         ++   + Y+A++H    T   ++   I R + +  +  V  +   + A T +K + +  N++L   +L TGRTHQIRVH   I + ++ DP+YG          GQ L A +L   HP   +E+    ++P+EF++ ++
  S:    23 MSLPMRLDRWLVSKRPEQSRARIQYFINAGLVLVNYKTAKAKTPLKTGDNIQIWMPPP---EPLIYLKPEKMNLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGL--LFHCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQESLVNLQIQIKEKIASRNYIAVIHGVPNTSEGKIVGHIGRDKLNRLKYAVVDEKSGRYACTYWKLLERLGNYSLMSFKLDTGRTHQIRVHCAHINHPILGDPLYGRCKKLPCKLDGQALHAVELGLFHPINGEEMKFEAELPQEFQKLLR 314
>gi|54020208|ref|YP_115967.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma hyopneumoniae 232] >gi|53987381|gb|AAV27582.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma hyopneumoniae 232] (304 aa)
Score = 309, Expect = 1.4e-26, Identities = 97/284 (34%), Positives = 160/284 (56%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEI-ILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVN-----INLDMPKEF 289
           R+DILV+   +LSR +A+  I    V +N  ++ K N  V    +I I  + K       L P + D EI+++D+ ++++NKP +++VHP   +  NTL N +   FDS +     D +R GIVHRLDK T GL++VAK+  + + F     +++I++ Y A++   +  + ++++ PI R   +  ++     ++K A T  + I  +    ++F+L + +L TGRTHQIR+H   I   +  DPIYG     K  + GQ L AYKL F      K++N        D+P+EF
  S:    17 RIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIRIFNDYK--RPKPQLEPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLE---QLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLKNPLKKTISFFNSKPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPIYGDPIYG----KKIDELGQRLHAYKLVF------KDLNGLSREFQADLPEEF 295
>gi|190893167|ref|YP_001979709.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D [Rhizobium etli CIAT 652] >gi|190698446|gb|ACE92531.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D [Rhizobium etli CIAT 652] (354 aa)
Score = 309, Expect = 1.4e-26, Identities = 99/289 (34%), Positives = 161/289 (55%)
  Q:     6 RLDILVSSKF--SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQ----KIEKKYLALLHNHLQTRTVEVDAPIKRVETS-TRREVSR--DIDAKEARTIFKEINKYKNF-------TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD  ++++     SRS  K  I++  V++ G++I+ P  KV          E  + E +  TP  +DI  +I+YED  +++++KP  ++VHP S + + TL N + +      +   G   R GIVHRLDK T G+++VAK+  +    +  F D      +E+ Y A++    ++ T  VDAP+ R     TRR V R    DA EA T ++ I ++          +L E  L TGRTHQIRVH   I + ++ D +YG          P+ I K       Q L A+ L+F HP + + ++  + +P +  E ++
  S:    37 RLDAWLTAQLGEEFSRSRIKVLIKDGQVSMRGQLITDPQRKVRAGDSF----EITLPEPEDPTPQGEDIPLDILYEDDDLIVISKPAGLVVHPGSGNWTGTLVNALIH-HCGATLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYRAIVWGRPRSLTGTVDAPLGRATGDRTRRAVKRPDSQDADEAITHYEVIERFHETPDATALASLVECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFRTKANLLPEDIRKVVNRFDRQALHAFMLQFEHPRSGELMHFEVPLPDDMVELVE 350
>gi|186475732|ref|YP_001857202.1| RluA family pseudouridine synthase [Burkholderia phymatum STM815] >gi|184192191|gb|ACC70156.1| pseudouridine synthase, RluA family [Burkholderia phymatum STM815] (436 aa)
Score = 309, Expect = 1.5e-26, Identities = 93/293 (31%), Positives = 156/293 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD +++  F   SRS  +  IE   V V+G+  +K    V   + I L  + ++ E    T     +++VYED  ++++NKP  ++VHP + + S T+ N + + +        G P R GIVHRLDK T GL++VA++L++     +    + ++++YLAL+  ++      +DAPI R     TR  V      K ART F+ I+    + +  +    +L TGRTHQIRVH   I + ++ DP+YG     ++          Q L A++L  +HP T + +    D+P +  E  +  G
  S:    92 ERLDKVLAKVFPEFSRSRLQSWIEAQRVHVDGQP-AKIRQPVPLGASIELVPD-LLPEQLAFTAEPVPLDVVYEDDTLVVINKPAGLVVHPAAGNWSGTVLNGLLHRYGDAAA---GLP-RAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPDDGT-IDAPIGRDPRERTRMAVVTGAAGKPARTHFRRIDSTVWERQPVSAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLALVHPKTGRTMQWRADVPGDIAELSEALG 389
>gi|45440505|ref|NP_992044.1| 23S rRNA pseudouridine synthase D [Yersinia pestis biovar Microtus str. 91001] >gi|51595196|ref|YP_069387.1| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis IP 32953] >gi|145600172|ref|YP_001164248.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Pestoides F] >gi|162420770|ref|YP_001607807.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Angola] >gi|170025566|ref|YP_001722071.1| RluA family pseudouridine synthase [Yersinia pseudotuberculosis YPIII] >gi|186894214|ref|YP_001871326.1| RluA family pseudouridine synthase [Yersinia pseudotuberculosis PB1/+] >gi|45435362|gb|AAS60921.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Microtus str. 91001] >gi|51588478|emb|CAH20086.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA) [Yersinia pseudotuberculosis IP 32953] >gi|145211868|gb|ABP41275.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis Pestoides F] >gi|162353585|gb|ABX87533.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis Angola] >gi|169752100|gb|ACA69618.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis YPIII] >gi|186697240|gb|ACC87869.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis PB1/+] (325 aa)
Score = 309, Expect = 1.5e-26, Identities = 96/289 (33%), Positives = 157/289 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKY------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I ++ VTVNGK I+KP  KV    E++  + +I E+ +   P +  ++IVYED  IL++NKP  ++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   ++ T    VD PI R  ++ R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG     PK  + +          Q L A  L+  HP +  ++  +  +P++  E I
  S:    18 QRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKV-LGGELVAIDAQIEEDAR-WAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPEIM-----DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNM-TAGGRVDEPISR-HSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFIAILRGFDRQALHATMLRLYHPISGIQMEWHAALPEDMVELI 309
>gi|160888049|ref|ZP_02069052.1| hypothetical protein BACUNI_00457 [Bacteroides uniformis ATCC 8492] >gi|156862548|gb|EDO55979.1| hypothetical protein BACUNI_00457 [Bacteroides uniformis ATCC 8492] (356 aa)
Score = 309, Expect = 1.5e-26, Identities = 90/279 (32%), Positives = 145/279 (51%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           SR+  +   +   V  NGK + K + KV     I +  ++   E +V+ P    ++IVYEDKY+++VNKP  ++VHP   +   TL N I +        Y+ +   +G+VHR+DK T GL+++AK+ D+       F ++  +++Y AL+  +++     V   I R      +  V  D   K A T ++ + +    TL E  L TGRTHQIRVH + I + + ND  YG   I K T + +Y               L A  L F+HP T +E+    ++P +    I K+
  S:    55 SRNRIQKAADAGFVMANGKAV-KSSYKVKPMDVITVMMDRPRYENEVI-PEDIPLDIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNP-DYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRRYRALVWGNVEQDEGTVVGNIGRNPRDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDTCPRQALHAMTLGFVHPVTGEEMYFTSELPDDMTRLIDKW 346
>gi|196040729|ref|ZP_03108028.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus NVH0597-99] >gi|196028519|gb|EDX67127.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus NVH0597-99] (307 aa)
Score = 309, Expect = 1.6e-26, Identities = 82/246 (33%), Positives = 136/246 (55%)
  Q:    53 LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           L+    +EE   + P   ++++VYED ++LIVNKP  +  HP       TLAN++ + +  K     G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y AL+   ++ +   +DA I R    +TRR VS   D        +E  K +N TL  ++L TGRTHQIRVH  +  N ++ D +YG +     TKY   Q L A K+ F+HP T++E+ +++  P +  + +K++ +
  S:    66 LQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAFHYQMK-----GLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ-----TKYMSRQALHAMKINFLHPITKEEIEVDIPFPTKLNDTMKEFQR 304
>gi|94310295|ref|YP_583505.1| ribosomal large subunit pseudouridine synthase D [Ralstonia metallidurans CH34] >gi|93354147|gb|ABF08236.1| ribosomal large subunit pseudouridine synthase D [Ralstonia metallidurans CH34] (403 aa)
Score = 309, Expect = 1.6e-26, Identities = 93/289 (32%), Positives = 158/289 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKII-SKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPL-----RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYK----NFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           +RLD L++  FS  SRS  +  IE+  V V+G+   +K + ++ ++ E+   + +   E+   T     +++VYED  +L++NKP  ++VHP + + S T+ N +           + DP      R GIVHRLDK T GL++VA++L +     +    + +++ YLAL+          +DAPI R     TR  +      K +RT F+ +          ++   +L TGRTHQIRVH E I + ++ DP+Y     +K T+ GQ                L AY+L  +HP T ++++   + P++ +  I
  S:    69 ERLDKLLARHFSEFSRSRIQQWIEDGAVRVDGEPSRAKASVQMGQKIEV---QPQAAPESMAFTAEDVPLDVVYEDDAMLVINKPAGLVVHPAAGNWSGTVLNGL----------LHRDPSAARLPRAGIVHRLDKETSGLMVVARTLVAQTDLVRQLAARTVKRTYLALVWGETPDDGT-IDAPIGRDPRERTRMAIVHTNSGKPSRTHFETLGTVPLGRGKVSMVMCQLETGRTHQIRVHFESIGHPLVGDPVY-----HKATQRGQRPAIRVPLPVPFTRQALHAYRLGLVHPVTGRKMSWEAEPPEDLQALI 365
>gi|163755786|ref|ZP_02162904.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida OT-1] >gi|161324307|gb|EDP95638.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida OT-1] (346 aa)
Score = 309, Expect = 1.6e-26, Identities = 86/225 (38%), Positives = 129/225 (57%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREV---SRDID-AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           I+IVYED  +L+VNKP  ++VHP   + S TL N + Y FD+     N  P   G+VHR+DK T GL++VAK+ ++     K F D+  E+ Y AL+  +++     V+  I R   +  +       D D  K A T +K + +    TL   +L TGRTHQIRVH + I + + ND  YG + I K T + +Y               L A  L FIHP T ++++ N ++P +  E I+K+
  S:    97 IDIVYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALIYHFDNLPKNSNERP---GLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSERIYYALVWGNVEEDEGTVEGNIGRHPKNRLQNTVFFGEDADKGKPAVTHYKVLERLGYVTLVSCQLETGRTHQIRVHMKHIGHTLFNDERYGGERILKGTTFTKYKQFVENCFKILPRQALHAKTLGFIHPRTGEKMSFNSEVPSDIAECIEKW 337
>gi|157336135|emb|CAO61965.1| unnamed protein product [Vitis vinifera] (385 aa)
Score = 309, Expect = 1.6e-26, Identities = 100/288 (34%), Positives = 151/288 (52%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKI---VEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREV-----SRDIDAKEARTIFK--EINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           RLD  +SS+   +SR+  +  I + LV+VN +I       VD+ S +I   +K+   + E + L    +DI  +IVYED+++L+VNKP  ++VHP   + S TL N I +   S+        +R GIVHRLDK T GL++VAK   S    ++ F    I + Y++L        +  V+ P+ R   +  R       S    A+ A + +K  EI       L E  L TGRTHQIR HA+++   ++ D +YG    N        L A  L F HP T K V+ +   P++F E +
  S:    78 RLDSWISSRIIGISRARVQSSIRSGLVSVNDRI-------VDKVSHVIRAGDKVNCTISELQPLRAEPEDIPLDIVYEDEHVLVVNKPAHMVVHPAPGNASGTLVNGILH-HCSQNCGTCETNIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHSIHRVYISLTSGVPTPLSGRVEIPVGRDPNNRIRMTAVPGPSNSGQARHAASRYKVIEILAAGGSALVEWRLETGRTHQIRAHAKYLGIPLLGDEVYGGTK-NMALLDRPCLHAVALGFNHPKTGKNVHFSCQPPEDFAEIL 369
>gi|34497647|ref|NP_901862.1| pseudouridine synthase D [Chromobacterium violaceum ATCC 12472] >gi|34103503|gb|AAQ59865.1| pseudouridine synthase D [Chromobacterium violaceum ATCC 12472] (363 aa)
Score = 308, Expect = 1.7e-26, Identities = 89/286 (31%), Positives = 154/286 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-PKH-INKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +RLD  ++      SRS     +++ LV V+G++++ P TK+   E+ E+ L+   +  E     P   D+ IV+ED++IL++NKP  ++VHP + + S TL N ++ +      +       R GIVHRLDK T GL++VAK+L +     +    + +++ Y A+    +      +DA I R   +  +        K A T  + + ++ + +  E +L TGRTHQIRVH     + +  DP+YG P+H +++    G      Q L A+ L  +HP T +E +    +P +F+
  S:    34 ERLDAALAKLLPDYSRSRLTQWVKDGLVKVDGQVVA-PKTKMLGGEKLEVTLQ---LTNEEMAFQPEPMDLPIVFEDEHILVINKPAGLVVHPAAGNWSGTLLNGLLHHCPALASVP------RAGIVHRLDKDTSGLMVVAKTLPAQTELVRQLQARTVKRVYRAIADGVVPFDGT-IDANIGRDANNRLKMAVLKFGGKPAITHIRVLERFASHSHVECKLETGRTHQIRVHMREAGHPLAGDPVYGNPRHKMDEEIAAGVKALGRQALHAFALALVHPATGEERSWKAPLPDDFR 320
>gi|103487227|ref|YP_616788.1| pseudouridine synthase, RluD [Sphingopyxis alaskensis RB2256] >gi|98977304|gb|ABF53455.1| ribosomal large subunit pseudouridine synthase D [Sphingopyxis alaskensis RB2256] (376 aa)
Score = 308, Expect = 1.8e-26, Identities = 73/225 (32%), Positives = 121/225 (53%)
  Q:    71 DIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRR-EVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKH-----INKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           D+ I YED ++++++KP  ++VHP + +L  T+ N + +   + ++   G   R GIVHR+DK T GL++ AK   +     K F    I+++YLA+           VDA + R  T+ ++  V      K A T ++ +   +  TL E  L TGRTHQ+RVH   I + ++ DP+YG        + K   +  Q L A  L FIHP T   + ++ ++P + +E I +
  S:   143 DLVIAYEDAHLIVIDKPAGMVVHPAAGNLDGTMVNALLH-HCAGQLSGIGGVARPGIVHRIDKDTSGLIVAAKHDKAHEGLAKQFAAHSIDRRYLAIATGRPMPANGTVDAALGRSATNRKKMAVVAAGRGKHALTHYRTVEPLQGATLIECRLETGRTHQVRVHMAHIGHPLVGDPVYGRARKPLSDVLKARNFARQALHAAHLGFIHPVTGNRIALDSELPADMRELIDE 373
>gi|72080790|ref|YP_287848.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma hyopneumoniae 7448] (289 aa)
Score = 308, Expect = 1.8e-26, Identities = 96/284 (33%), Positives = 157/284 (55%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETK----VLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           R+DILV+   +LSR +A+  I    V +N  ++ K N  V    +I     KI  + K     L P + D EI+++D+ ++++NKP +++VHP   +  NTL N +   FDS +     D +R GIVHRLDK T GL++VAK+  + + F     +++I++ Y A++   +  + ++++ PI R   +  ++     ++K A T  + I  +    ++F+L + +L TGRTHQIR+H   I   +  DPIYG     K  + GQ L AYKL F             D+P+EF
  S:     2 RIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKI-----KIFNDYKRPKPQLEPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLE---QLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLKNPLKKTISFFNSKPAITNVELIKHFNYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPIYGDPIYG----KKIDELGQRLHAYKLVF-KDLNGLSREFQADLPEEF 280
>gi|57241079|ref|ZP_00369026.1| Ribosomal large subunit pseudouridine synthase D [Campylobacter lari RM2100] >gi|57018000|gb|EAL54775.1| Ribosomal large subunit pseudouridine synthase D [Campylobacter lari RM2100] (320 aa)
Score = 308, Expect = 1.8e-26, Identities = 96/291 (32%), Positives = 157/291 (53%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID---AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLV-AYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +RLDI +S     SRS     I+ N + +N KI +K + K+ ++ EI +    I E  +  TP + DIEI+YED  +L++NK  +I+VH  S     TL + + +   +     NG+  R G+VHRLDK T G +I+AK+  +        LD+ + + YLAL    L+   +  +  I R   +  ++++ +     AK A+T F  +   KN +L   +L+TGRTHQIR H      +++ D +YG K      KY + ++ AY + FIHP T++ + I   M  +F + +K+
  S:    10 ERLDIFLSDILKQSRSQVAKLIKENCIYINEKIENKSSKKIKQKDEISIFLPLIKEAKESYTP-EFDIEILYEDDDVLVLNKAPNIVVHGASSVKEATLVDWLLHKGYTLS-NLNGEH-RAGLVHRLDKGTSGAIIIAKNNQAHQFLANQLLDKSMGRFYLALSELPLKNDKMSNEKAIMRCPNNRLKKITTNTKNPLAKNAKTDFINLLSAKNCSLIAAKLYTGRTHQIRTHLADFNRYILGDELYGYK---GKIKYNRVMLHAYLIYFIHPRTKELMFIKAPMFDDFYQILKE 298
>gi|170703044|ref|ZP_02893871.1| pseudouridine synthase, RluA family [Burkholderia ambifaria IOP40-10] >gi|170132052|gb|EDT00553.1| pseudouridine synthase, RluA family [Burkholderia ambifaria IOP40-10] (365 aa)
Score = 308, Expect = 1.8e-26, Identities = 90/293 (30%), Positives = 152/293 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD  ++  F   SRS  +  IE   V ++G   +K    V   + I L  + ++ E    TP    ++++YED  +L++NKP  ++VHP + + S T+ N + + +        G P R GIVHRLDK T GL++VA++L +     +    + ++++Y AL+   +      +DAPI R     TR  V      K ART F+ ++    + +  +  + +L TGRTHQIRVH   + + ++ DP+YG     ++          Q L A++L  +HP T K +     +P++    I   G
  S:    27 ERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAP-AKIRQPVPLGARIELVPD-LLPEQLAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYGDAAA---GLP-RAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDGT-IDAPIGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGLVHPLTGKTMQWRCPLPEDMNALIAALG 324
>gi|121534815|ref|ZP_01666635.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans Nor1] >gi|121306610|gb|EAX47532.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans Nor1] (301 aa)
Score = 308, Expect = 1.9e-26, Identities = 97/292 (33%), Positives = 146/292 (50%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +T   D L S+  SL++ + K K +   V +NG  +    T V    EI +       +   LTP K  + IVYED ++LIVNKP  ++VHPTS     TLA+ I Y   SK       P     +HRLD+ T GLV +AK     +A +     + +++ YLA++     +    +DAPI R   S  + V R  D + A T+++ ++ +   +L E+EL TGRTHQIRVH   I + ++ D +YG           Q L A  L F HP T K + +   +P +  + I+
  S:    12 STSVRDFLKSAGISLTQ-LRKIKRQGQ-VLINGHPVKSFQTPVSSGDEISID----YGDDSCLTPMKMPLHIVYEDDFLLIVNKPAGLLVHPTSDPTEPTLAHGILYYLHSKGALGAFHP-----IHRLDRNTSGLVAIAKHPHIQHALSGGGA-KGLKRLYLAVVTGIPSSLMGRIDAPIGRHPNSIIKRVVRS-DGQPAITLYRVLSTFSMASLVELELLTGRTHQIRVHLSHIGHPLLGDDLYGGA---TDLIRRQALHAASLSFRHPATDKVLTLTSPLPPDLADLIQ 287
>gi|78356492|ref|YP_387941.1| pseudouridine synthase, RluD [Desulfovibrio desulfuricans subsp. desulfuricans str. G20] >gi|78218897|gb|ABB38246.1| pseudouridine synthase, RluD [Desulfovibrio desulfuricans G20] (578 aa)
Score = 308, Expect = 1.9e-26, Identities = 87/293 (29%), Positives = 152/293 (51%)
  Q:     5 QRLDILVSSKFS---LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVET-STRREVSRDIDAKEARTIFKEI------NKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----------PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +R D  +++  +   +SR   +  I +  + ++  + + P TK+     I+   E        ++P + ++E++Y D ++L++NKP  + VHP       TL + + + F   + +   +  R GIVHR+DK T GL+++A +  +  A +  F  ++I K+YLAL+    +  + E+DAP+ R  T  TR  V R    +EA + ++ +           +TL  V + TGRTHQIRVH +   + +  D +YG           P      T+  Q L A+K+ F HP T   +   L  P +F   I+  G
  S:    52 ERADRFIAAALAGDAISRGKIQRAISDGQLLIDNTVCTSPKTKLKSGQHIVFSMEA---PAACVSPEEGELEVLYRDAHMLVINKPAGLTVHPAPSCPEGTLVHRLLHHFPELEAQ---EGFRPGIVHRIDKDTSGLLLIALTEKARLALSDAFAGRRIHKEYLALVKGIPEGDSGEIDAPVGRHPTHKTRMAVVR--GGREALSTWRVLLADPHGGGGTGWTLVAVRIHTGRTHQIRVHMQHTGHPLWGDALYGGMPGREELQTTPALAQTATR--QMLHAWKISFDHPVTGAPMQFTLPPPADFGTLIRDLG 355
>gi|71893806|ref|YP_279252.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma hyopneumoniae J] (289 aa)
Score = 308, Expect = 1.9e-26, Identities = 96/284 (33%), Positives = 157/284 (55%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETK----VLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           R+DILV+   +LSR +A+  I    V +N  ++ K N  V    +I     KI  + K     L P + D EI+++D+ ++++NKP +++VHP   +  NTL N +   FDS +     D +R GIVHRLDK T GL++VAK+  + + F     +++I++ Y A++   +  + ++++ PI R   +  ++     ++K A T  + I  +    ++F+L + +L TGRTHQIR+H   I   +  DPIYG     K  + GQ L AYKL F             D+P+EF
  S:     2 RIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKI-----KIFNDYKRPKPQLEPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLE---QLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLKNPLKKTISFFNSKPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPIYGDPIYG----KKIDELGQRLHAYKLVF-KDLNGLSREFEADLPEEF 280
>gi|196035329|ref|ZP_03102734.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus W] >gi|195992006|gb|EDX55969.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus W] (307 aa)
Score = 308, Expect = 1.9e-26, Identities = 82/246 (33%), Positives = 136/246 (55%)
  Q:    53 LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           L+    +EE   + P   ++++VYED ++LIVNKP  +  HP       TLAN++ + +  K     G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y AL+   ++ +   +DA I R    +TRR VS   D        +E  K +N TL  ++L TGRTHQIRVH  +  N ++ D +YG +     TKY   Q L A K+ F+HP T++E+ +++  P +  + +K++ +
  S:    66 LQVRMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAFHYQMK-----GLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ-----TKYMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDTMKEFQR 304
>gi|144227643|gb|AAZ44541.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma hyopneumoniae J] (304 aa)
Score = 308, Expect = 1.9e-26, Identities = 96/284 (33%), Positives = 157/284 (55%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETK----VLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           R+DILV+   +LSR +A+  I    V +N  ++ K N  V    +I     KI  + K     L P + D EI+++D+ ++++NKP +++VHP   +  NTL N +   FDS +     D +R GIVHRLDK T GL++VAK+  + + F     +++I++ Y A++   +  + ++++ PI R   +  ++     ++K A T  + I  +    ++F+L + +L TGRTHQIR+H   I   +  DPIYG     K  + GQ L AYKL F             D+P+EF
  S:    17 RIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKI-----KIFNDYKRPKPQLEPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLE---QLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLKNPLKKTISFFNSKPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPIYGDPIYG----KKIDELGQRLHAYKLVF-KDLNGLSREFEADLPEEF 295
>gi|144575467|gb|AAZ53825.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma hyopneumoniae 7448] (304 aa)
Score = 308, Expect = 2.0e-26, Identities = 96/284 (33%), Positives = 157/284 (55%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETK----VLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKY----KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           R+DILV+   +LSR +A+  I    V +N  ++ K N  V    +I     KI  + K     L P + D EI+++D+ ++++NKP +++VHP   +  NTL N +   FDS +     D +R GIVHRLDK T GL++VAK+  + + F     +++I++ Y A++   +  + ++++ PI R   +  ++     ++K A T  + I  +    ++F+L + +L TGRTHQIR+H   I   +  DPIYG     K  + GQ L AYKL F             D+P+EF
  S:    17 RIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKI-----KIFNDYKRPKPQLEPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLE---QLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLKNPLKKTISFFNSKPAITNVELIKHFNYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPIYGDPIYG----KKIDELGQRLHAYKLVF-KDLNGLSREFQADLPEEF 295
>gi|28211276|ref|NP_782220.1| ribosomal large subunit pseudouridine synthase D [Clostridium tetani E88] >gi|28203716|gb|AAO36157.1| ribosomal large subunit pseudouridine synthase D [Clostridium tetani E88] (307 aa)
Score = 308, Expect = 2.0e-26, Identities = 98/290 (33%), Positives = 154/290 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKV---DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +RLD+ +       SRS  K   ++  + VN +I  K N KV   D    ++ KEE I  E + +     D+ I+YED+ I+++NKP  ++VHP   +   TL N +  +   K +       R GIVHR+DK T G++++AK+  +         D  + + Y+AL    ++     +D  + R   S R + +   + K A T +K IN+Y N +L E  L TGRTHQIRVH  +I + ++ DP YG K   K    GQ L A KL FIHP   + +  + ++P+EFK+ ++
  S:    17 ERLDLFIVENLKDKSRSFIKKLSDDKGIMVNDEI-KKVNYKVKCGDIVKVLLPKEEGIYLEKENM-----DLNILYEDEDIIVINKPQGMVVHPGVGNTKGTLVNGL--LAHCKSLSNINGEERPGIVHRIDKDTSGILVIAKTNRAHEHLANQLKDHSMLRVYMALTEGVIKEDMGTIDKDLGR-NPSDRIKFAVVDEGKRAVTHYKVINRYNNNSLIECRLETGRTHQIRVHMSYIGHPIVGDPTYGYKR-QKFKLKGQMLHAKKLGFIHPTNGEYMEFDSEIPEEFKKILE 300
>gi|153834660|ref|ZP_01987327.1| ribosomal large subunit pseudouridine synthase D [Vibrio harveyi HY01] >gi|156973324|ref|YP_001444231.1| 23S rRNA pseudouridine synthase D [Vibrio harveyi ATCC BAA-1116] >gi|148868912|gb|EDL67970.1| ribosomal large subunit pseudouridine synthase D [Vibrio harveyi HY01] >gi|156524918|gb|ABU70004.1| hypothetical protein VIBHAR_01005 [Vibrio harveyi ATCC BAA-1116] (325 aa)
Score = 308, Expect = 2.1e-26, Identities = 93/287 (32%), Positives = 154/287 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG-----------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           QRLD  ++  F+  SRS  K  +    V VNG++++KP T+V    EI L+ E  +E+ +        ++IVYED+ I+++NKP D +VHP +     T+ N + + + D  ++       R GIVHRLDK T GL++VAK++ +     +    + I ++Y A+    + T   +VD PI R  ++ R  ++     K A T ++    ++  T   + L TGRTHQIRVH  ++++ ++ D  YG +    T               Q L A  L+F HP T +E+  +  +P +  E
  S:    18 QRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTRVMGGEEITLQAE--LEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAEVP------RAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRM-TAGGKVDKPIGR-HSTKRTLMAVAPMGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASEELTEMIRGFDRQALHAVMLRFDHPVTGEELEFHAPVPDDMVE 307
>gi|167836421|ref|ZP_02463304.1| ribosomal large subunit pseudouridine synthase D [Burkholderia thailandensis MSMB43] (344 aa)
Score = 308, Expect = 2.1e-26, Identities = 92/293 (31%), Positives = 154/293 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD  ++  F   SRS  +  IE++ V V+G   +K    V   + I L  + ++ E    TP    + IVYED+ I++V+KP  ++VHP + + S TL N + + +        G P R GIVHRLDK T GL++VA++L +     +    + ++++Y AL+   +  +   +DAPI R     TR  V      K ART F+ ++    + +  +    +L TGRTHQIRVH   + + ++ DP+YG     ++          Q L A++L  +HP T + +     +P +    ++  G
  S:    17 ERLDKALAQLFPEFSRSRLQQWIESDRVRVDGAP-AKIRQPVPLGATIELLPD-LLPEQLAFTPEPVPLSIVYEDEAIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAA----GLP-RAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDKGT-IDAPIGRDPRERTRMAVVTGAAGKPARTHFRAVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLGLVHPATGRTMQWRAPLPADLAALVEALG 313
>gi|116253506|ref|YP_769344.1| putative ribosomal large subunit pseudouridine synthase D [Rhizobium leguminosarum bv. viciae 3841] >gi|115258154|emb|CAK09255.1| putative ribosomal large subunit pseudouridine synthase D [Rhizobium leguminosarum bv. viciae 3841] (341 aa)
Score = 308, Expect = 2.1e-26, Identities = 100/289 (34%), Positives = 165/289 (57%)
  Q:     6 RLDILVSSKF--SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQ----KIEKKYLALLHNHLQTRTVEVDAPIKRVETS-TRREVSR--DIDAKEARTIFKEINKYKN-------FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTK-YG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD  ++++     SRS  K  I++  V + G+ ++ P  KV          E  + E +  TP  +DI  +I++ED  +++++KP+ ++VHP + + + TL N +I +  D+  +   G   R GIVHRLDK T G+++VAK+  +    +  F D      +E+ Y A++    +T +  VDAP+ R     TRR V R    DA EA T ++ I ++          +L E  L TGRTHQIRVH   I + ++ D +YG          P+ I K    +G Q L A+ L+F HP T + ++  + +P +  E ++
  S:    24 RLDAWLTAQVGEEFSRSRIKALIKDGQVLLRGEPVTDPQRKVRTGDSF----ELTLPEPEDPTPQGEDIPLDILHEDDDVIVISKPSGLVVHPGAGNWTGTLVNALIHHCSDT--LSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTMPLERAYQAIVWGRPRTLSGTVDAPLGRATGDRTRRAVKRPDSQDADEAITHYQVIERFHEKPDATAFASLVECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANLLPEEIRKVVNGFGRQALHAFMLQFEHPRTGEIMHFEVPLPDDMVELVE 337
>gi|110639847|ref|YP_680057.1| ribosomal large subunit pseudouridine synthase D [Cytophaga hutchinsonii ATCC 33406] >gi|110282528|gb|ABG60714.1| ribosomal large subunit pseudouridine synthase D [Cytophaga hutchinsonii ATCC 33406] (348 aa)
Score = 308, Expect = 2.1e-26, Identities = 98/295 (33%), Positives = 156/295 (52%)
  Q:     2 KNTQRLDILVSSKFSL-SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVS---RDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           ++  R+D  + S+    +RS  ++ IE + V VN K  +K + KV     I +       E  VL P    ++IVYED  ILIVNK   ++VHP   + + TL N + Y F++     NG  +R G++HR+DK T GL+++AK+  +     K F D  IE+ Y A+       ++  +   + R  T  R+ V+    + D K A T +K +  Y    L +  L TGRTHQIR H + I + + ND  YG   + K T  G+Y               L A  L FIHP T++++  + ++P + +  + K+
  S:    31 QSLMRIDKFLMSRIQYATRSRIQYGIEIDSVKVNDKS-TKASYKVRPGDVITISLPHPPRE-DVLIPEDIPLDIVYEDDQILIVNKKPGMVVHPAHGNWTGTLVNALAYHFENLPTHVNGK-IRPGLIHRIDKDTSGLLVIAKTDYAMTFMAKQFADHSIERTYYAICWGVPDPKSGTIKNYLGR-STKDRKLVTTYENEEDGKLAITHYKTLAAYHYVALIQCNLETGRTHQIRAHMKSIGHSLFNDMSYGGNSVVKGTVTGKYKQFVENCFKLLPRQALHAKTLGFIHPTTKEKMQFDSELPADMQAVLDKW 340
>gi|157376631|ref|YP_001475231.1| lysozyme [Shewanella sediminis HAW-EB3] >gi|157319005|gb|ABV38103.1| Lysozyme [Shewanella sediminis HAW-EB3] (323 aa)
Score = 308, Expect = 2.1e-26, Identities = 96/284 (33%), Positives = 157/284 (55%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINK---TTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  ++  F   SR+  K  I+   V ++G +  KP  KV  E ++I  E  +VEETK       D++IVYED +IL++NK   ++VHP + +   TL N + +   + ++       R GIVHRLDK T GL++VAK++++          ++I ++Y A++   L +    VD PI R  T  R  ++   + K A T ++   K++  T   + L +GRTHQIRVH   I + ++ DP+YG     PK ++        G   Q L A +L+  HP+T + ++    +P++
  S:    18 QRLDQTLADLFPDYSRTRIKEWIQAGWVYIDGTVSIKPREKV-LEGQVIQVEATLVEETKA-KAQAIDLDIVYEDDHILVINKQAGLVVHPGAGNSDGTLMNALLHHCPNIELV-----PRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVQGSLISGGT-VDEPIDRHPTK-RTHMAVVHNGKPAMTHYRVAEKFRAHTRLRLRLESGRTHQIRVHMSHIGHTLVGDPVYGGRPRPPKGVSPEFFEIYMGFKRQALHAIRLELAHPYTCEIMSWQAPVPED 304
>gi|86144060|ref|ZP_01062398.1| ribosomal large subunit pseudouridine synthase D [Flavobacterium sp. MED217] >gi|85829520|gb|EAQ47984.1| ribosomal large subunit pseudouridine synthase D [Leeuwenhoekiella blandensis MED217] (344 aa)
Score = 307, Expect = 2.3e-26, Identities = 96/279 (34%), Positives = 154/279 (55%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEI-ILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDID-AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           +R+  +   +N  + VNG ++ K N KV     + +L E    E   +LTP    ++IV+ED  +L+VNKP  ++VHP   + S TL N + Y FD+     +G P   G+VHR+DK T GL++VAK+ ++     K F D+  E++Y+A++  +++     V+  I R  +   +  V  D D  KEA T +K + +    T    +L TGRTHQIRVH + I + + ND  YG   I K T + +Y               L A  L F HP T + +  +  +P++ +  I+K+
  S:    45 TRNKIQQAAKNGNIQVNGAVV-KQNHKVKANDVVRVLFEHPPYE--FLLTPEDIPLDIVFEDDTLLVVNKPAGMVVHPGHGNYSGTLINALIYHFDNLPENSSGRP---GLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSEREYIAIVWGNVEEDQGTVEGHIGRHPKNRMQNTVYEDGDQGKEAVTHYKVLERLGYVTKISCKLETGRTHQIRVHMKHIGHTLFNDERYGGDAILKGTTFTKYKQFVENCFKVLPRQALHAKTLGFEHPKTGEWMRFDSAIPEDMEACIEKW 335
>gi|172040870|ref|YP_001800584.1| pseudouridylate synthase D [Corynebacterium urealyticum DSM 7109] >gi|171852174|emb|CAQ05150.1| pseudouridylate synthase D [Corynebacterium urealyticum DSM 7109] (314 aa)
Score = 307, Expect = 2.5e-26, Identities = 89/290 (30%), Positives = 146/290 (50%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEE---SEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPT-SYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           R+D  +S    LSR++         +T  GK + K +  V  +     +   E  +  E   L    + ++I+Y D  ++ VNKP  +  HPT  ++     A +    F   +I  +G P R GIV RLD  T G++IVA S  ++    + F +++++K Y AL+  H    +  +DAPI R  ++  R   RD D K A T +  +  ++  +L  V L TGRTHQIRVH   + + +  DP+YG  P    K     Q+L A  L+F HP T + + I+   P++ ++ + +
  S:    19 RVDAGLSKLLGLSRTVVADLAAAGDITAEGKSLGKSDRLVAGQWLDVTLPAPERDLAAEPPQLV---EGMDILYSDDDVIAVNKPVGVAAHPTLGWEGPTVTAGLAAAGF---RISTSGPPERKGIVQRLDVGTSGVMIVAASERAYTHLKRAFRNREVQKIYHALVQGHPDPTSGTIDAPIGRHPSAGWRFAVRD-DGKHAVTHYDTLEAHRQASLLRVNLETGRTHQIRVHFSSLHHPLCGDPMYGSDPALSEKLGLIRQWLHAVSLRFEHP-TGRMMQIDSPYPEDLQQALDR 306
>gi|52144044|ref|YP_082785.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus E33L] >gi|51977513|gb|AAU19063.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus E33L] (307 aa)
Score = 307, Expect = 2.5e-26, Identities = 82/246 (33%), Positives = 134/246 (54%)
  Q:    53 LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           L+    +EE   + P   ++ +VYED ++LIVNKP  +  HP+      TLAN++ + F     +  G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y AL+   ++ +   +DA I R    +TRR VS   D        +E  K +N TL  ++L TGRTHQIRVH  +  N ++ D +YG       TKY   Q L A K+ F+HP T++E+ +++  P +  + +K + +
  S:    66 LQVHMFMEEEYDVEPEYGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFHF-----QMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG-----GGTKYMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDTMKAFQR 304
>gi|168719660|ref|ZP_02751937.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. EC4206] >gi|168793777|ref|ZP_02818784.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. EC4042] (282 aa)
Score = 307, Expect = 2.6e-26, Identities = 89/262 (33%), Positives = 142/262 (54%)
  Q:    33 VNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           VNGK+  KP  KV    ++ +  E  +EE     P    ++IVYED+ I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    VD PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ DP+YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:     3 VNGKLCDKPKEKVLGGEQVAINAE--IEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 266
>gi|167575781|ref|ZP_02368655.1| hypothetical protein BvalV_03156 [Borrelia valaisiana VS116] (326 aa)
Score = 307, Expect = 2.6e-26, Identities = 86/279 (30%), Positives = 155/279 (55%)
  Q:     2 KNTQRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIIS-KPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKL----------KFIHPFTQKEVN 280
           +N  RLD+ +SS    L+RS  K +        NGK +  K +  V ++ EI+++ ++ + +   L P    I I+YED  I+++NKP  I+ HP      +T+ N + Y   S KI +NG+ +R GIVHRLDK T G++I AK++ +     + F D++  K Y+A++  +  + +  +++ I R + + ++        K++ T ++ +  +  ++L  ++  TGRTHQ+RVH +++   ++ D +YG +      K    L +YKL          KFI  F ++ VN
  S:    12 ENALRLDLYLSSNLEVLTRSQIKRRNVEAFKKSNGKFLKIKLSKPVFKDDEILIEFDEEISQIDCLRPNNIPIAIIYEDSNIIVLNKPQGILSHPGISHWDDTVVNFLLYHIKSLKIDFNGEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFRDKRTNKVYIAIVKGNFNSFSGSIESFIDRDKHNRKKFAVSKDRGKKSLTEYRLLLNFGGYSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKITLMLHSYKLEIDVGKNSFEKFISEFPKRFVN 301
>gi|118444250|ref|YP_878581.1| ribosomal large subunit pseudouridine synthase D [Clostridium novyi NT] >gi|118134706|gb|ABK61750.1| ribosomal large subunit pseudouridine synthases, RluD subfamily [Clostridium novyi NT] (301 aa)
Score = 307, Expect = 2.6e-26, Identities = 86/239 (35%), Positives = 135/239 (56%)
  Q:    60 EETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTI--FKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           EE + + P K  ++++YEDK I+++NKP  I+VHPT    + TL+N + Y F  K    N + + + +V+RLD  T GLV++AK+  S  A ++        K YLA++H +L+ ++  ++ PI RV   T R V   ID +  R++  FK +  Y++  L E+ L TGRTHQIRVH   I + +  D +YG +      +  Q L AYKL+  HP   + + +  D+P + K  I K  K
  S:    71 EENQDIVPEKMHLDVIYEDKDIVVINKPKGIVVHPTKRHQNGTLSNGVLYYFKEK----NENSI-VRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVKSYLAIVHGNLKEKSGVINKPIYRVGEGTLRRV---IDERGQRSVTRFKVVESYEDADLVELTLETGRTHQIRVHLSSIGHPIYGDSLYGKEEHEYIDR--QALHAYKLQIPHPKDGRILKLESDLPDDMKNLISKLKK 301
>gi|86148440|ref|ZP_01066731.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. MED222] >gi|85833794|gb|EAQ51961.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. MED222] (324 aa)
Score = 307, Expect = 2.7e-26, Identities = 102/284 (35%), Positives = 162/284 (57%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWK-KDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID--AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINK--TTKY----GQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  V+  F+  SRS  K  + +  + V+G++I+KP T V     IIL+ E   EE      W+ +DI  +IVYED  +L++NKP D++VHP +     T+ N +  +F   +I    +  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+    +    V V+  I R   +T+R +  D++   K A T ++    ++  T   + L TGRTHQIRVH  ++++ ++ D  YG     PK  ++  TT       Q L A  LKF+HP T +EV  +  +P +
  S:    18 QRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGEAIILQAELADEER-----WEAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGTILNAL--LFHYPQI---AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMTAGGV-VEKGISR--HATKRTL-MDVNELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPKGASEELTTMIRSFDRQALHAVMLKFVHPITGEEVEFHAPVPND 304
>gi|170718793|ref|YP_001783975.1| RluA family pseudouridine synthase [Haemophilus somnus 2336] >gi|168826922|gb|ACA32293.1| pseudouridine synthase, RluA family [Haemophilus somnus 2336] (324 aa)
Score = 307, Expect = 2.8e-26, Identities = 102/285 (35%), Positives = 161/285 (56%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYGQYLVAYK--------LKFIHPFTQKEVNINLDMPKEF 289
           QRLD  ++  F   SRS  K  IE +LV VNG+II+   TKV    E++    +I EE++   P    + IVYED++IL++NKP D +VHP + +   T+ N + Y +   KI    +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+  +VD P+ R  T  R +++     K A T ++ + +++N+T   + L TGRTHQIRVH   I + ++ D  YG     PK  N + ++ Q +  +K        L   HP T + +     +P +F
  S:    17 QRLDQTLAELFPDYSRSRLKTWIEGDLVKVNGEIINVARTKV-YGGELVEICVEIEEESR-FEPENLPLNIVYEDEHILVINKPKDFVVHPGAGNQRGTVLNALLYHY--PKIV---EVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVQDLQKRKIIREYEAVAFG-VMTQGGKVDQPMSRHPTK-RTQMAVHPLGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHISHPLLGDQTYGGRPRPPK--NASEEFMQVMRDFKRQALHAIMLCLTHPITGEIMEWEAPLPDDF 304
>gi|171320446|ref|ZP_02909479.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5] >gi|171094306|gb|EDT39380.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5] (369 aa)
Score = 307, Expect = 2.8e-26, Identities = 90/293 (30%), Positives = 151/293 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD  ++  F   SRS  +  IE   V ++G   +K    V   + I L  + ++ E    TP    ++++YED  +L++NKP  ++VHP + + S T+ N + + +        G P R GIVHRLDK T GL++VA++L +     +    + ++++Y AL+   +      +DAPI R     TR  V      K ART F+ ++    + +  +  + +L TGRTHQIRVH   + + ++ DP+YG     ++          Q L A++L  +HP T K +     +P +    I   G
  S:    27 ERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAP-AKIRQPVPLGARIELVPD-LLPEQLAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYGDAAA---GLP-RAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDGT-IDAPIGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGLVHPLTGKTMQWRCPLPDDMNALIAALG 324
>gi|172060753|ref|YP_001808405.1| RluA family pseudouridine synthase [Burkholderia ambifaria MC40-6] >gi|171993270|gb|ACB64189.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MC40-6] (407 aa)
Score = 307, Expect = 2.8e-26, Identities = 90/293 (30%), Positives = 151/293 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD  ++  F   SRS  +  IE   V ++G   +K    V   + I L  + ++ E    TP    ++++YED  +L++NKP  ++VHP + + S T+ N + + +        G P R GIVHRLDK T GL++VA++L +     +    + ++++Y AL+   +      +DAPI R     TR  V      K ART F+ ++    + +  +  + +L TGRTHQIRVH   + + ++ DP+YG     ++          Q L A++L  +HP T K +     +P +    I   G
  S:    69 ERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAP-AKIRQPVPLGARIELVPD-LLPEQLAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYGDAAA---GLP-RAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDGT-IDAPIGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGLVHPLTGKTMQWRCPLPDDMNALIAALG 366
>gi|115351782|ref|YP_773621.1| RluA family pseudouridine synthase [Burkholderia ambifaria AMMD] >gi|115281770|gb|ABI87287.1| ribosomal large subunit pseudouridine synthase D [Burkholderia ambifaria AMMD] (405 aa)
Score = 307, Expect = 2.8e-26, Identities = 90/293 (30%), Positives = 151/293 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD  ++  F   SRS  +  IE   V ++G   +K    V   + I L  + ++ E    TP    ++++YED  +L++NKP  ++VHP + + S T+ N + + +        G P R GIVHRLDK T GL++VA++L +     +    + ++++Y AL+   +      +DAPI R     TR  V      K ART F+ ++    + +  +  + +L TGRTHQIRVH   + + ++ DP+YG     ++          Q L A++L  +HP T K +     +P +    I   G
  S:    69 ERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAP-AKIRQPVPLGARIELVPD-LLPEQLAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYGDAAA---GLP-RAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDGT-IDAPIGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGLVHPLTGKTMQWRCPLPDDMNALIAALG 366
>gi|165923990|ref|ZP_02219822.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii RSA 334] >gi|165916576|gb|EDR35180.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii RSA 334] (323 aa)
Score = 307, Expect = 2.9e-26, Identities = 98/289 (33%), Positives = 157/289 (54%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQT-RTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHIN-------KTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD +++  F   SRS  ++ I    V V+G   +K   KV E   I ++ +  +E  +   P    ++++YED+ +L++NKP  +IVHP +     TL N + +   S  +       R GI+HRLDK T GL+++A++L S +A  K    ++I ++Y A++   L + RT+E  AP+ R      R    +   + A T F+ I +Y+  T   V+L TGRTHQIRVH   I + V  DP+YG     P H++       KT K  Q L A  L+F HP  Q+ +  +  +P +    ++
  S:    20 RLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEAQ--LEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLSVV-----PRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIE--APVGRHPIHRTRMAVVEF-GRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHPVAGDPVYGSHVGIPVHLSDPLQTALKTLKR-QALHAATLQFSHPVDQRPMACHAPLPADMAHLLE 311
>gi|119946871|ref|YP_944551.1| pseudouridine synthase, RluA family protein [Psychromonas ingrahamii 37] >gi|119865475|gb|ABM04952.1| ribosomal large subunit pseudouridine synthase D [Psychromonas ingrahamii 37] (322 aa)
Score = 307, Expect = 2.9e-26, Identities = 95/286 (33%), Positives = 150/286 (52%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINK---TTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           RLD  V+S F   SR+  K  I  ++V ++G++I++P  KV     + +  + ++E+  V    K  +EIVYED  IL++NKP  ++VHP + +   T+ N + + F         +  R GIVHRLDK T GL++VAK++ +          ++I ++Y A+      T    V+API R +    +        K A T ++   KY+  T   + L TGRTHQIRVH   I + +  DP+YG     PK  ++    T  G   Q L A  L+  HP T + +  +  +P +  E
  S:    19 RLDQAVASLFPDYSRTRIKEWILADMVKIDGEVINRPREKVYTGQTVGV--QAVLEDEVVFKAQKIKLEIVYEDDDILVINKPAGLVVHPGAGNPDGTVLNALLHHFPQII-----EVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVTSLQAREITREYEAIAMGGF-TAGGFVEAPIGRDKVHRVKMAVNSTGGKHALTHYRVSEKYRAHTRLRLRLETGRTHQIRVHMMHIGHVLTGDPVYGGRPRPPKGASEALLATLRGFRRQALHATMLRLAHPITGEIMEWHAPLPADMAE 308
>gi|84393596|ref|ZP_00992349.1| ribosomal large subunit pseudouridine synthase D [Vibrio splendidus 12B01] >gi|84375805|gb|EAP92699.1| ribosomal large subunit pseudouridine synthase D [Vibrio splendidus 12B01] (324 aa)
Score = 307, Expect = 2.9e-26, Identities = 102/284 (35%), Positives = 162/284 (57%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWK-KDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID--AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINK--TTKY----GQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  V+  F+  SRS  K  + +  + V+G++I+KP T V     IIL+ E   EE      W+ +DI  +IVYED  +L++NKP D++VHP +     T+ N +  +F   +I    +  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+    +    V V+  I R   +T+R +  D++   K A T ++    ++  T   + L TGRTHQIRVH  ++++ ++ D  YG     PK  ++  TT       Q L A  LKF+HP T +EV  +  +P +
  S:    18 QRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGEAIILQAELADEER-----WEAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGTILNAL--LFHYPQI---AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMTAGGV-VEKGISR--HATKRTL-MDVNELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPKGASEELTTMIRSFDRQALHAVMLKFVHPITGEEVEFHAPVPND 304
>gi|42780479|ref|NP_977726.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus ATCC 10987] >gi|42736398|gb|AAS40334.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Bacillus cereus ATCC 10987] (307 aa)
Score = 306, Expect = 2.9e-26, Identities = 88/268 (32%), Positives = 147/268 (54%)
  Q:    31 VTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           VTVNG+   + N  + E+ +  L+    +EE   + P   ++++VYED ++LIVNKP  +  HP       TLAN++ + F     +  G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y AL+   ++ +   +DA I R    +TRR VS   D        ++  K +N TL  ++L TGRTHQIRVH  +  N ++ D +YG       TKY   Q L A K+ F+HP T++E+ +++  P +  + +K++ +
  S:    47 VTVNGEQ-RRWNELLKEDEK--LQVHMFMEEEYGVEPEYGELDVVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAFHF-----QMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDILYG-----GGTKYMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDTMKEFQR 304
>gi|118602363|ref|YP_903578.1| ribosomal large subunit pseudouridine synthase D [Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)] >gi|118567302|gb|ABL02107.1| ribosomal large subunit pseudouridine synthase D [Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)] (314 aa)
Score = 306, Expect = 2.9e-26, Identities = 93/259 (35%), Positives = 145/259 (55%)
  Q:    40 KPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           KP  KV    E+I    KI E+T         I++VYED+ I+IVNKP +++ HP   + + TLAN + + +DS     +    R GIVHRLDK T GL++VA+S  +    T+      I ++Y A+++ H+ +    VD PI R      R+   +   K+A T ++ I ++ + T  +V L TGRTHQIRVH  FI + +I DP+YG     PK  +K  K        Q L A KL  IHP + + ++  + +P++ ++ ++   K
  S:    50 KPKEKV-LGGEVITLSIKI-EKTNAWLAQDIVIDVVYEDEAIIIVNKPVNLVTHPGVSNWTGTLANALLH-YDSSLANLD----RAGIVHRLDKNTSGLMVVARSEYAQKYLTRQLQTHSISREYSAIVYGHMISGGT-VDKPIGRDPKDRIRQTVTE-SGKDALTHYRVIERFAHHTHVKVMLETGRTHQIRVHLSFIGHPLIADPMYGGKIRFPKKADKQLKNSLKNFNRQTLHAKKLTLIHPTSTELMSWKVPLPQDMQDLLQVLAK 310
>gi|83648561|ref|YP_436996.1| pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis KCTC 2396] >gi|83636604|gb|ABC32571.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis KCTC 2396] (319 aa)
Score = 306, Expect = 2.9e-26, Identities = 92/284 (32%), Positives = 157/284 (55%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTT-----KYG-QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD+  S      SRS  ++ I+   + VNGK + KP  KV E  ++ L  E   +      P   D+  V+ED+++L++NK  D +VHP +     T+ N + +           +  R GIVHRLDK T GL+++AK+L + N+  +    +++ ++Y  +++  L    V V+A I R     R++++     K+A T ++ I +++ FT   ++L TGRTHQIRVH   I + ++ DP+YG     PK ++  T      +G Q L A  L+  HP T + ++  + +P++
  S:    18 QRLDMAASELMPEYSRSRIQNWIKQGALRVNGKQV-KPKEKVIEGDQVELDVELEAQGDWEAQPIALDV--VFEDEHLLVINKQADFVVHPAAGHSDGTVVNAVLH-----HCPALSELPRAGIVHRLDKDTTGLMVIAKTLIAHNSLVEQLQAREMGREYECVVYGELTGGGV-VEAAIGR-HPQNRQKMAVTRGGKDAVTHYRLIRRWRGFTHLRLKLETGRTHQIRVHMAHIHHSILGDPLYGSRPRLPKGLSAETIEYLQTFGRQALHAKALELSHPVTGELLSWEVGLPED 303
>gi|33239671|ref|NP_874613.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus subsp. marinus str. CCMP1375] >gi|33237196|gb|AAP99265.1| 23S RNA-specific pseudouridylate synthase [Prochlorococcus marinus subsp. marinus str. CCMP1375] (318 aa)
Score = 306, Expect = 2.9e-26, Identities = 95/284 (33%), Positives = 145/284 (51%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRR-EVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           RLD  LVS +   SR+  +  IE+ LV VNG I  K  T +    EI L      E    L P K  ++I++ED +I+++NKP  + VHP   +   TL N ++ +  D   I  NG  LR GIVHRLDK T G +++AKS ++          +   ++Y+AL+H         + API R     ++  V  D   ++A T ++   +  +++L   +L TGRTHQIRVH+  I + ++ DP Y       T   GQ L A +L   HP ++ ++     +P  F
  S:    28 RLDRWLVSQRSEQSRARIQKFIEDGLVLVNG-IQGKSKTPLRTGDEIQLWVPP-PEPLPYLKPQKMHLDIIFEDSHIIVINKPAGLTVHPAPGNKDRTLVNGLLHHCTDLPGI--NGK-LRPGIVHRLDKDTTGCIVIAKSQEALVNLQVQIQKRIASRRYIALVHGVPHGDKGIISAPIGRHPIDRKKYAVVNDGSGRDACTHWELKERLGDYSLLSFKLETGRTHQIRVHSAHIGHPILGDPTYSRCKKLPTKLTGQVLHAIQLGLQHPISKTDILFEAPLPDTF 309
>gi|154148379|ref|YP_001406840.1| RluA family pseudouridine synthase [Campylobacter hominis ATCC BAA-381] >gi|153804388|gb|ABS51395.1| pseudouridine synthase, RluA family [Campylobacter hominis ATCC BAA-381] (357 aa)
Score = 306, Expect = 3.0e-26, Identities = 105/295 (35%), Positives = 156/295 (52%)
  Q:     1 MKNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIK---YIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTI---------------FKEIN---KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + ++ RLDI ++    +SR+   + IE N + VN  + +K + K+  +  + +      E   +      DIEI+YED  +L++NKP+ ++VHP       TLA  +K   Y+  S     NGD  R GIVHRLDK T G ++VAK+  +         D+ + + YLA L   L+   V VD  I R  ++  ++     +   AR+                FK +N      NF L   +LFTGRTHQIRVH   I  H+I D +YG K      K   +L AY L F HP T +++ I+  +P EFK  I+K
  S:    19 LSSSIRLDIFLTKILKISRNKILNLIEENHIFVNNSVQNKASFKLKNDDIVGINFPLKKENENLKQNANFDIEILYEDDDLLVLNKPSGVVVHPAKSVKEPTLAEWLKQKKYMLSS----INGDE-RAGIVHRLDKQTSGAILVAKTDFAHVKLAAQLKDKSMGRIYLAFLDLALK-ENVCVDRFIARNPSNRLKKAVVPPNENGARSAKSAFLNIANDTILQNFKPLNFSQNQTNFNLIAAKLFTGRTHQIRVHLSSINRHIIGDFLYGFKSDFDKIKR-IFLHAYLLYFTHPRTNRQILISAKIPSEFKNLIEK 327
>gi|54310131|ref|YP_131151.1| 23S rRNA pseudouridine synthase D [Photobacterium profundum SS9] >gi|90414902|ref|ZP_01222867.1| putative ribosomal large subunit pseudouridine synthase D [Photobacterium profundum 3TCK] >gi|46914570|emb|CAG21349.1| putative ribosomal large subunit pseudouridine synthase D [Photobacterium profundum SS9] >gi|90324016|gb|EAS40610.1| putative ribosomal large subunit pseudouridine synthase D [Photobacterium profundum 3TCK] (324 aa)
Score = 306, Expect = 3.0e-26, Identities = 92/283 (32%), Positives = 150/283 (53%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           RLD +++  +   SRS  K  I  N+V+VNG+I++KP  K+    E+ +K E  +E+          ++IVYED++IL++NKP D +VHP +     T+ N +  +F    +    +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T    V+ PI R  T        ++  K A T ++    ++  T   + L TGRTHQIRVH  ++ + ++ D IYG     P+H +            Q L A  L+  HP T + +     +P +
  S:    19 RLDQVIAELYPDYSRSRVKEWILKNMVSVNGEIVNKPRLKMMGGEELFIKAE--IEDEVRWVAQDIPLDIVYEDEHILVINKPRDFVVHPGAGTPDRTVLNAL--LFHCPAL---AEVPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEAIAMGKM-TGGGTVEKPIGRHATKRICMAVHEL-GKPAITHYRVAEHFREHTRLVLRLETGRTHQIRVHMSYMSHPLVGDAIYGGRPRPPRHASDELILALRSFDRQALHARMLRLSHPITGELMEWRAPLPND 304
>gi|163802429|ref|ZP_02196322.1| ribosomal large subunit pseudouridine synthase D [Vibrio campbellii AND4] >gi|159173730|gb|EDP58545.1| ribosomal large subunit pseudouridine synthase D [Vibrio campbellii AND4] (325 aa)
Score = 306, Expect = 3.1e-26, Identities = 92/287 (32%), Positives = 156/287 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG-----------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           QRLD  ++  F+  SRS  K  + +  V VNG++++KP T+V    EI L+ E  +E+ +        ++IVYED+ I+++NKP D +VHP +     T+ N + + + D  ++       R GIVHRLDK T GL++VAK++ +     +    + I ++Y A+    + T   +V+ PI R  ++ R  ++     K A T ++   +++  T   + L TGRTHQIRVH  ++++ ++ D  YG +    T               Q L A  L+F HP T +E+  +  +P +  E
  S:    18 QRLDQAIAELFADFSRSRLKEWLLDGKVHVNGEVVTKPRTRVMGGEEITLQAE--LEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDCTVLNALLHHYPDIAEVP------RAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRM-TAGGKVEQPIGR-HSTKRTLMAVAPLGKPAVTHYRVAERFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASEELTAMIRGFDRQALHAVMLRFEHPITGEELEFHAPIPDDMVE 307
>gi|49477179|ref|YP_035519.1| ribosomal large subunit pseudouridylate synthase D [Bacillus thuringiensis serovar konkukian str. 97-27] >gi|49328735|gb|AAT59381.1| ribosomal large subunit pseudouridylate synthase D [Bacillus thuringiensis serovar konkukian str. 97-27] (307 aa)
Score = 306, Expect = 3.1e-26, Identities = 88/268 (32%), Positives = 146/268 (54%)
  Q:    31 VTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           VTVNG+   + N ++ E  +  L+    +EE   + P   ++ +VYED ++LIVNKP  +  HP+      TLAN++ + F     +  G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y AL+   ++ +   +DA I R    +TRR VS   D        +E  K +N TL  ++L TGRTHQIRVH  +  N ++ D +YG       TKY   Q L A  + F+HP T++E+ +++  P +  + +K++ +
  S:    47 VTVNGEQ-RRWNERLKEGDK--LQVHMFMEEEYDVEPEYGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFHF-----QMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG-----GGTKYMSRQALHAMTINFLHPITKEEIEVDVPFPTKLNDTMKEFQR 304
>gi|163939199|ref|YP_001644083.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis KBAB4] >gi|163861396|gb|ABY42455.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis KBAB4] (307 aa)
Score = 306, Expect = 3.1e-26, Identities = 86/266 (32%), Positives = 145/266 (54%)
  Q:    31 VTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           VTVNG+   + N  + E  +  L+    +EE   + P   ++ +V+ED ++LIVNK   +  HP+  + + TLAN++ + F     +  G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y AL+   ++ +   +DA I R    +TRR VS   D        ++  K +N TL  ++L TGRTHQIRVH  +  N ++ D +YG +    T   GQ L A K+ F+HP T++E+ +++  P    + +KK+
  S:    47 VTVNGEQ-RRWNELLKEGDK--LQVHMFMEEEYGVEPEYGELNVVFEDDHVLIVNKQGQMDTHPSEKNGTGTLANLVAFHF-----QMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKKQNATLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ---TTYMSGQALHAMKINFLHPITKEEIVVDVPFPTNLNDTMKKF 302
>gi|16123434|ref|NP_406747.1| 23S rRNA pseudouridine synthase D [Yersinia pestis CO92] >gi|22124820|ref|NP_668243.1| 23S rRNA pseudouridine synthase D [Yersinia pestis KIM] >gi|108808759|ref|YP_652675.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Antiqua] >gi|108810984|ref|YP_646751.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Nepal516] >gi|153997673|ref|ZP_02022773.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis CA88-4125] >gi|165926534|ref|ZP_02222366.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Orientalis str. F1991016] >gi|165936735|ref|ZP_02225302.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Orientalis str. IP275] >gi|166010204|ref|ZP_02231102.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Antiqua str. E1979001] >gi|166213045|ref|ZP_02239080.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Antiqua str. B42003004] >gi|167398582|ref|ZP_02304106.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Antiqua str. UG05-0454] >gi|167421637|ref|ZP_02313390.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Orientalis str. MG05-1020] >gi|167423313|ref|ZP_02315066.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Mediaevalis str. K1973002] >gi|167470273|ref|ZP_02334977.1| 23S rRNA pseudouridine synthase D [Yersinia pestis FV-1] >gi|34395805|sp|Q8ZBV7|RLUD_YERPE Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|21957646|gb|AAM84494.1|AE013693_10 suppressor of ftsH mutation [Yersinia pestis KIM] >gi|108774632|gb|ABG17151.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis Nepal516] >gi|108780672|gb|ABG14730.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis Antiqua] >gi|115348913|emb|CAL21870.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis CO92] >gi|149289310|gb|EDM39390.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis CA88-4125] >gi|165915384|gb|EDR33994.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Orientalis str. IP275] >gi|165921462|gb|EDR38659.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Orientalis str. F1991016] >gi|165991111|gb|EDR43412.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Antiqua str. E1979001] >gi|166205832|gb|EDR50312.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Antiqua str. B42003004] >gi|166960556|gb|EDR56577.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Orientalis str. MG05-1020] >gi|167051086|gb|EDR62494.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Antiqua str. UG05-0454] >gi|167057483|gb|EDR67229.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis biovar Mediaevalis str. K1973002] (325 aa)
Score = 306, Expect = 3.2e-26, Identities = 96/289 (33%), Positives = 156/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKY------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I ++ VTVNGK I+KP  KV    E++  + +I E+ +   P +  ++IVYED  IL++NKP  ++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   ++ T    VD PI R  ++ R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG     PK  + +          Q L A  L+  HP    ++  +  +P++  E I
  S:    18 QRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKV-LGGELVAIDAQIEEDAR-WAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPEIM-----DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNM-TAGGRVDEPISR-HSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFIAILRGFDRQALHATMLRLYHPIRGIQMEWHAALPEDMVELI 309
>gi|50122269|ref|YP_051436.1| 23S rRNA pseudouridine synthase D [Pectobacterium atrosepticum SCRI1043] >gi|49612795|emb|CAG76245.1| ribosomal large subunit pseudouridine synthase D [Erwinia carotovora subsp. atroseptica SCRI1043] (325 aa)
Score = 306, Expect = 3.3e-26, Identities = 94/289 (32%), Positives = 153/289 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I +N V +NG +I+KP  KV     + +  + ++EE          ++IVYED+ IL++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+    + T    V+ PI R   + R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG     PK      I     +  Q L A  L+F HP T  ++  +  +P++  + I
  S:    18 QRLDQALAELFPDYSRSRIKEWILDNRVQINGNVINKPKEKVLGGESVAI--DALIEEEARWEAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEIV-----DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSM-TAGGMVEQPIAR-HATKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHIDHPLVGDQLYGGRPRPPKGASDDFIEMLRGFDRQALHATMLRFYHPITGIQMEWHAALPQDMVDLI 309
>gi|110802739|ref|YP_699398.1| pseudouridylate synthase family protein, yabo [Clostridium perfringens SM101] >gi|110683240|gb|ABG86610.1| pseudouridylate synthase family protein, yabo [Clostridium perfringens SM101] (298 aa)
Score = 306, Expect = 3.3e-26, Identities = 95/293 (32%), Positives = 153/293 (52%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + +++   +  +  LS  + +    +  + V+G +  K N  V    EI ++  K  +E++ + P K DIEIVYED  IL++NK   ++VHPT    + TLAN I Y F     K +     + +V RLD  T GL+I+ K+  +    +      K +K+YLA++H +L+ +   ++ PI R    T + V  D   +E+ T +K I  Y    L E  L TGRTHQIRVH   + + +  D +YG +     ++  Q L AY L F  P T+K +++  D+P++ KE I K
  S:    13 DKRKIREFLKEELGLSSRLIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSK--KESQNIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYF-----KESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISR--QALHAYGLDFYSPKTKKSLSLRADLPEDMKELINK 294
>gi|154483515|ref|ZP_02025963.1| hypothetical protein EUBVEN_01219 [Eubacterium ventriosum ATCC 27560] >gi|149735425|gb|EDM51311.1| hypothetical protein EUBVEN_01219 [Eubacterium ventriosum ATCC 27560] (301 aa)
Score = 305, Expect = 3.9e-26, Identities = 92/279 (32%), Positives = 145/279 (51%)
  Q:    17 LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +SRS  +  +++N + +N K + K N KV    +I +   K VE   V       ++I+YED   LIVNKP D++VHP     + TL N + Y   +     NG  LR GIVHR+DK T G +I+ K+  S N   +      I +KY+ ++   ++  +  ++API R   + +       + KEA T +K + ++  +T  E +L TGRTHQIRVH   I + ++ D +Y         + GQ L A  + FIHP T++ V     +P E+ E++ K
  S:    27 VSRSFIQKLLKDNEILLNDKPV-KANYKVQPSDKININIPKPVEANIVAE--NIPLDIIYEDDDFLIVNKPKDMVVHPAPGHYTGTLVNGLMYHCKNHLSNING-VLRPGIVHRIDKDTTGALIICKNDYSHNFIAEQLKVHSITRKYVGIVQGVVKDESGTINAPIGRHPVNRKEMAINHKNGKEAVTHYKVLKRFDKYTFMEFQLETGRTHQIRVHMASIHHPLLGDTVYNHNKCPFKLE-GQCLHAKTIGFIHPTTKEYVEFEAPIP-EYMEHLLK 299
>gi|148827314|ref|YP_001292067.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae PittGG] >gi|148718556|gb|ABQ99683.1| SfhB [Haemophilus influenzae PittGG] (324 aa)
Score = 305, Expect = 3.9e-26, Identities = 98/289 (33%), Positives = 156/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYGQYLVAYK--------LKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  IE +LV +N +I + P  KV   E+ EI ++    VE+     P    + IVYED  I+++NKP D++VHP + + + T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+   VD P+ R   + R  ++     K A T ++ +  Y+N+T   + L TGRTHQIRVH   I + ++ D  YG     PK  N +  + + L  +K        L+  HP T + +     +P +F E +
  S:    17 QRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGEKIEITVE----VEDETRFEPENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI-----AEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASG-IMTKGGTVDQPMAR-HATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPK--NASEDFMEVLRNFKRQALHAVMLRLSHPITGEMMEWYAPLPDDFVELL 308
>gi|49184224|ref|YP_027476.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne] >gi|65318659|ref|ZP_00391618.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus anthracis str. A2012] >gi|165870408|ref|ZP_02215063.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0488] >gi|166991937|ref|ZP_02258397.1| RNA pseudouridylate synthase [Bacillus cereus AH820] >gi|167634370|ref|ZP_02392691.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0442] >gi|167639342|ref|ZP_02397614.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0193] >gi|170686762|ref|ZP_02877982.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0465] >gi|170706270|ref|ZP_02896731.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0389] >gi|177651449|ref|ZP_02934238.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0174] >gi|190568721|ref|ZP_03021625.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis Tsiankovskii-I] >gi|49178151|gb|AAT53527.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne] >gi|164713903|gb|EDR19425.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0488] >gi|167512781|gb|EDR88155.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0193] >gi|167530258|gb|EDR92984.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0442] >gi|170128804|gb|EDS97670.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0389] >gi|170669285|gb|EDT20028.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0465] >gi|172082727|gb|EDT67790.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis str. A0174] >gi|190560137|gb|EDV14118.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus anthracis Tsiankovskii-I] (307 aa)
Score = 305, Expect = 4.0e-26, Identities = 81/246 (32%), Positives = 135/246 (54%)
  Q:    53 LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           L+    +EE   + P   ++++VYED ++LIVNKP  +  HP       TLAN++ + +  K     G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y AL+   ++ +   +DA I R    +TRR VS   D        +E  K +N T   ++L TGRTHQIRVH  +  N ++ D +YG +     TKY   Q L A K+ F+HP T++E+ +++  P +  + +K++ +
  S:    66 LQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAFHYQMK-----GLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQNVTFVTLQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ-----TKYMSRQALHAMKINFLHPITKEEIEVDIPFPTKLNDTMKEFQR 304
>gi|182623983|ref|ZP_02951771.1| pseudouridine synthase, RluA family [Clostridium perfringens D str. JGS1721] >gi|177910876|gb|EDT73230.1| pseudouridine synthase, RluA family [Clostridium perfringens D str. JGS1721] (298 aa)
Score = 305, Expect = 4.0e-26, Identities = 94/293 (32%), Positives = 155/293 (52%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + +++   +  +  LS  + +    +  + V+G +  K N  V    EI ++  K  +E++ + P K DIEIVYED  IL++NK   ++VHPT    + TLAN I Y F     K +     + +V RLD  T GL+I+ K+  +    +      K +K+YLA++H +L+ +   ++ PI R    T + V  D   +E+ T +K I  Y+   L E  L TGRTHQIRVH   + + +  D +YG +  +  ++  Q L AY L F  P T++ +++  D+P++ KE I K
  S:    13 DKRKIREFLKEELGLSSRLIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSK--KESQNIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYF-----KESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-DERGQESITHYKVIESYEGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEDFISR--QALHAYGLDFYSPKTKEPLSLRADLPEDMKELINK 294
>gi|71083312|ref|YP_266031.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1062] >gi|71062425|gb|AAZ21428.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1062] (326 aa)
Score = 305, Expect = 4.0e-26, Identities = 97/289 (33%), Positives = 158/289 (54%)
  Q:     2 KNTQRLDILVSSKFSL-SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN-----FTLAEVELFTGRTHQIRVHAEFIKNHVIND---PIYGPKHINKTTKYG--------QYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +N  RLD+ ++ + +L SR+  K+ I    + +N +II+ P+ KV    EI L+  +  E +  L P+   ++IVYED  +LI+NKP  II+HP + +   T+ N + + ++   +   GD LR GIVHR+DK T GL+++AK+ ++    +  F +  I + Y  L+   L+  + ++D  I R   + +     +   K A T +K I  ++N      +L E  L TGRTHQIRVH   + N ++ D        K  N  T           Q+L A  L FIHP T +E+     +P+E +
  S:    13 ENNLRLDVFINKRENLISRTRIKNLILKEKLKINDQIINSPSKKVLSGDEINLQIPEPKEAS--LKPYNFKLQIVYEDDDLLIINKPAGIIMHPGAGNYDETIVNALMH-YNKDSLSTIGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFSEHTITRVYQLLIWGKLRPSSGKIDTFITRSSKNRQMMEVSNSKGKRAITNYKTIEIFENDKTPTLSLVECRLETGRTHQIRVHMTHMGNSIMGDGKYKKKYKKLKNIDTNLENLIYKLDRQFLHAQTLGFIHPRTNEEMVFTSILPQELE 315
>gi|166982065|ref|ZP_02253512.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus AH187] >gi|168163115|ref|ZP_02598348.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus H3081.97] (307 aa)
Score = 305, Expect = 4.3e-26, Identities = 85/246 (34%), Positives = 140/246 (56%)
  Q:    53 LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKY---KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           L+    +EE   + P   ++ +VYED ++LIVNKP  +  HP+      TLAN++ + F     +  G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y AL+   ++ +   +DA I R    +TRR VS   D  +A T +K + KY   +N TL  ++L TGRTHQIRVH  +  N ++ D +YG       TKY   Q L A K+ F+HP T++E+ +++  P +  + +K++ +
  S:    66 LQVHMFMEEEYGVEPEYGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFHF-----QMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGD--QAITYYK-VEKYFRKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG-----GGTKYMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDTMKEFQR 304
>gi|157369129|ref|YP_001477118.1| 23S rRNA pseudouridine synthase D [Serratia proteamaculans 568] >gi|157320893|gb|ABV39990.1| pseudouridine synthase, RluA family [Serratia proteamaculans 568] (325 aa)
Score = 305, Expect = 4.4e-26, Identities = 96/289 (33%), Positives = 151/289 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINK---TTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I +N V VNGK I+KP  KV     + +  +  +EE     P    + IVYED  IL++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    + I ++Y A+    + T    V+ PI R  ++ R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG     PK  +     T  G   Q L A  L+  HP +  ++  +  +P++  + I
  S:    18 QRLDQALAELFPDYSRSRIKDWILDNRVQVNGKTINKPKEKVLGGETVAIDAQ--IEEDARWEPQDIALNIVYEDSDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARDITREYEAVAIGTM-TAGGTVEEPISR-HSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDAFIATLRGFDRQALHATMLRLYHPISGIQMEWHAPLPQDMVDLI 309
>gi|55980377|ref|YP_143674.1| ribosomal large subunit pseudouridine synthase D [Thermus thermophilus HB8] >gi|55771790|dbj|BAD70231.1| ribosomal large subunit pseudouridine synthase D [Thermus thermophilus HB8] (308 aa)
Score = 305, Expect = 4.4e-26, Identities = 90/283 (31%), Positives = 145/283 (51%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK--HINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           RLD  V+   S+SR+ A+  I+   V V  +++ KP  ++  E        + VEE  ++ P    I I+YED+ +L +NKP  ++ HP     S T+ N++   +     K   + +R GIVHRLDK T G+++VAK         + F D+ + K+YLA+   H   R   + API R      +     + A+ A T F+ +     + L E    TGRTHQIRVH +++   ++ D +YG K  HI +     Q L AY+L+  HP T + + +   +P++
  S:    10 RLDQAVAEALSVSRAKAQAWIQAGRVRVGDRVVLKPAYRLKGEE----VAVEPVEEAPMVLPEDLPIPILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLLARYYGPVEKGPPELVRPGIVHRLDKDTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAITEGH--PREGVLIAPIGRHPRERHKMHVGGLAARYAETEFQVLATAGPYALVEARPHTGRTHQIRVHLKYLGAPILGDELYGRKSPHIGR-----QALHAYELRIPHPRTGRILELLAPVPQD 283
>gi|46198348|ref|YP_004015.1| ribosomal large subunit pseudouridine synthase D [Thermus thermophilus HB27] >gi|46195970|gb|AAS80388.1| ribosomal large subunit pseudouridine synthase D [Thermus thermophilus HB27] (300 aa)
Score = 305, Expect = 4.5e-26, Identities = 90/283 (31%), Positives = 145/283 (51%)
  Q:     6 RLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK--HINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           RLD  V+   S+SR+ A+  I+   V V  +++ KP  ++  E        + VEE  ++ P    I I+YED+ +L +NKP  ++ HP     S T+ N++   +     K   + +R GIVHRLDK T G+++VAK         + F D+ + K+YLA+   H   R   + API R      +     + A+ A T F+ +     + L E    TGRTHQIRVH +++   ++ D +YG K  HI +     Q L AY+L+  HP T + + +   +P++
  S:     2 RLDQAVAEALSVSRAKAQAWIQAGRVRVGDRVVLKPAYRLKGEE----VAVEPVEEAPMVLPEDLPIPILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLLARYYGPVEKGPPELVRPGIVHRLDKDTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAITEGH--PREGVLIAPIGRHPRERHKMHVGGLAARYAETEFQVLATAGPYALVEARPHTGRTHQIRVHLKYLGAPILGDELYGRKSPHIGR-----QALHAYELRIPHPRTGRILELLAPVPQD 275
>gi|120437019|ref|YP_862705.1| ribosomal large subunit pseudouridine synthase D [Gramella forsetii KT0803] >gi|117579169|emb|CAL67638.1| ribosomal large subunit pseudouridine synthase D [Gramella forsetii KT0803] (354 aa)
Score = 305, Expect = 4.7e-26, Identities = 82/233 (35%), Positives = 135/233 (57%)
  Q:    64 VLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDID----AKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           +L P    ++IVYED  +L+VNK   ++VHP   + S TL N + + FD+     N    R G+VHR+DK T GL++VAK+ ++    +K F D+  E++Y+A++  +L      ++  I R   +  + +  + D     K A T +K + +    TL   +L TGRTHQIRVH ++I + + ND  YG   I K T + +Y               L A  L F+HP T++ ++ N D+P++  + I+K+
  S:    93 LLVPEDIPLDIVYEDDTLLVVNKQAGMVVHPGHGNYSGTLINALVHHFDNLP---NNSSDRPGLVHRIDKDTSGLLVVAKTEEAMAHLSKQFFDKSSEREYVAIVWGNLAEEEGTIEGNIGRNPRNRLQNIVFEGDDVENGKAAVTHYKVLERLGYVTLVACKLETGRTHQIRVHMKYIGHTLFNDERYGGDRILKGTTFTKYKQFVDNCFKILPRQALHAKTLGFVHPKTEEWMSFNSDIPQDMVDCIEKW 341
>gi|152974818|ref|YP_001374335.1| RluA family pseudouridine synthase [Bacillus cereus subsp. cytotoxis NVH 391-98] >gi|152023570|gb|ABS21340.1| pseudouridine synthase, RluA family [Bacillus cereus subsp. cytotoxis NVH 391-98] (307 aa)
Score = 305, Expect = 4.7e-26, Identities = 80/241 (33%), Positives = 136/241 (56%)
  Q:    58 IVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           I EE  V+ P   ++++V+ED ++LIVNKP  +  HP+  + + TLAN+I + F     +  G   ++  +HRLDK T G V+ AK   +     +L +++ I++ Y+AL+   ++ R   +DA I R    +TRR VS   D        +E  K ++ TL  V+L TGRTHQIRVH  +  + ++ D +YG    N T    Q L A ++ F+HP T++E+ +++  P++  + ++ + K
  S:    72 IPEEYGVI-PEFGELDVVFEDDHVLIVNKPEQMDTHPSEKNGTGTLANLIAFHF-----QMQGLETKVRHIHRLDKDTTGGVVFAKHRLAGAIMDQLLMERNIKRTYMALVEGKMKKRKGTIDAAIGRDRHHATRRRVSPKGDRAVTHYTVEEYFKRQDTTLVTVQLETGRTHQIRVHMSYNGHPLLGDVLYGG---NVTYMSRQALHAMQIAFLHPITREEIIVDIPAPEKIDKLMQSFRK 304
>gi|18311104|ref|NP_563038.1| hypothetical protein CPE2122 [Clostridium perfringens str. 13] >gi|168215749|ref|ZP_02641374.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC 8239] >gi|18145787|dbj|BAB81828.1| conserved hypothetical protein [Clostridium perfringens str. 13] >gi|182382353|gb|EDT79832.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC 8239] (298 aa)
Score = 305, Expect = 4.8e-26, Identities = 94/293 (32%), Positives = 154/293 (52%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + +++   +  +  LS  + +    +  + V+G +  K N  V    EI ++  K  +E++ + P K DIEIVYED  IL++NK   ++VHPT    + TLAN I Y F     K +     + +V RLD  T GL+I+ K+  +    +      K +K+YLA++H +L+ +   ++ PI R    T + V  D   +E+ T +K I  Y    L E  L TGRTHQIRVH   + + +  D +YG +  +  ++  Q L AY L F  P T++ +++  D+P++ KE I K
  S:    13 DKRKIREFLKEELGLSSRLIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSK--KESQNIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYF-----KESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEDFISR--QALHAYGLDFYSPKTKEPLSLRADLPEDMKELINK 294
>gi|47566178|ref|ZP_00237206.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Bacillus cereus G9241] >gi|47556731|gb|EAL15062.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Bacillus cereus G9241] (307 aa)
Score = 304, Expect = 5.0e-26, Identities = 80/246 (32%), Positives = 137/246 (55%)
  Q:    53 LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           L+    +EE   + P   ++ +VYED ++LIVNKP  +  HP+      TLAN++ + +     +  G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y+AL+   ++ +   +DA I R    +TRR VS   D        ++  K +N TL  ++L TGRTHQIRVH  +  N ++ D +YG +     TKY   Q L A K+ F+HP T++E+ +++  P +  + +K++ +
  S:    66 LQVHMFMEEEYGVEPEYGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFHY-----QMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYVALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKNQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ-----TKYMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDTMKEFQR 304
>gi|193215325|ref|YP_001996524.1| pseudouridine synthase, RluA family [Chloroherpeton thalassium ATCC 35110] >gi|193088802|gb|ACF14077.1| pseudouridine synthase, RluA family [Chloroherpeton thalassium ATCC 35110] (346 aa)
Score = 304, Expect = 5.2e-26, Identities = 93/291 (31%), Positives = 156/291 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDA---KEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINK--------------TTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+D  ++ +  + +R+  +  IE + V VNGK I K N KV    EI +           L P    ++IV+ED+++L++NKP  ++VHP   + + TLA  + Y   ++  +   + LR GIVHRLDK T GL++VAK   +  A  K F ++  EK Y AL+    +  +  +   I R +   +   +   ++   K A T ++    +  F+L +++L TGRTHQIR H + + + + +D +YG K + K                   Q L A KL F HP T+  V     +P++ ++ I+K
  S:    35 ERIDKFLTRQVENATRNKVQEAIEESRVLVNGKPI-KSNYKVCPNDEIFVIFTH--PPAPDLEPENIPLDIVFEDEFLLVINKPAGMVVHPAYANWTGTLAGAVLYHTQNRLSETGKEALRPGIVHRLDKDTSGLIVVAKDDATHYALAKQFAERTTEKIYTALVWGCPKPPSGTIQTNIWRSKRDRKIMANYPFESETGKPAITDYEVKEDFHWFSLLDLQLHTGRTHQIRAHLQHLGHAIFSDEVYGGKSVRKLGFPQSEAFVRNLFQVIPRQALHAKKLGFKHPATENFVTFEASLPEDMEQAIQK 340
>gi|15894548|ref|NP_347897.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824] >gi|15024193|gb|AAK79237.1|AE007639_10 Pseudouridylate synthase family protein, yabo B.subtilis ortholog [Clostridium acetobutylicum ATCC 824] (299 aa)
Score = 304, Expect = 5.3e-26, Identities = 96/263 (36%), Positives = 149/263 (56%)
  Q:    33 VNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPI-KRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           VNGK + + + +V E  +I +   K   E++ + P K D+ IVYED  I+++NKP ++IVHPT      TL+N + Y F  K     G+   + +V+RLD  T GLV+VAK+  S  A  +       +K+Y+A++  +L +    +D PI K  E   RR +  D   +E+ T F+ + +YKN    ++ L TGRTHQIRVH   I N +I D +YG +  ++  K  Q L A+KL+F HP   + VNI + +P++ +  I K
  S:    45 VNGKTV-RLSYRVLEGDKIEVDVNK--PESQNVDPEKMDLNIVYEDSDIIVLNKPANMIVHPTKNYQHGTLSNGLLYYFREK-----GENCIVRLVNRLDMDTSGLVLVAKNQFSHMALARDMKLDTFKKEYIAVVRGNLSSLKGTIDKPIYKEEEEPIRRTI--DDRGQESITHFEVVERYKNADKVKLVLETGRTHQIRVHLSSIGNPIIGDSLYGEE--SELIKR-QALHAFKLQFPHPRDGRIVNIEVKLPEDIENLISK 295
>gi|169346799|ref|ZP_02865750.1| pseudouridine synthase, RluA family [Clostridium perfringens C str. JGS1495] >gi|169297081|gb|EDS79203.1| pseudouridine synthase, RluA family [Clostridium perfringens C str. JGS1495] (298 aa)
Score = 304, Expect = 5.5e-26, Identities = 95/293 (32%), Positives = 153/293 (52%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + +++   +  +  LS  + +    +  + V+G +  K N  V    EI ++  K  +E++ + P K DIEIVYED  IL++NK   ++VHPT    + TLAN I Y F     K +     + +V RLD  T GL+I+ K+  +    +      K +K+YLA++H +L+ +   ++ PI R    T + V  D   +E+ T +K I  Y    L E  L TGRTHQIRVH   + + +  D +YG +     ++  Q L AY L F  P T+K +++  D+P++ KE I K
  S:    13 DKRKIREFLKEELGLSSRLIRSAAIDKRIKVDG-VSVKMNYVVKTGEEIKIELSK--KESQNIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYF-----KESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISR--QALHAYGLDFYSPKTKKPLSLRADLPEDMKELINK 294
>gi|148552990|ref|YP_001260572.1| ribosomal large subunit pseudouridine synthase D [Sphingomonas wittichii RW1] >gi|148498180|gb|ABQ66434.1| ribosomal large subunit pseudouridine synthase D [Sphingomonas wittichii RW1] (321 aa)
Score = 304, Expect = 5.5e-26, Identities = 89/286 (31%), Positives = 154/286 (53%)
  Q:     6 RLD-ILVSSKFSLSRSIAKHKIENNLVT-VNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIV--YEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVS--RDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG---PKH---INKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           RLD  L ++  +LSR   K  I +  V+  +G +   P  KV   +   +    IV +        +DI +V  YED+++++++KP  ++VHP + +   TL N + +      +   G   R GIVHR+DK T GL++ AK+  +       F    I+++Y A++    +     VDAP+ R  T+ R++++   D   K A T +  I   +   L E  L TGRTHQ+RVH   + + ++ DP+YG   P+H   +N+   + Q L A +L FIHP T   ++ + ++P++ ++
  S:    20 RLDRALAAALPTLSRERLKALISSGQVSHADGALARDPAMKVAPGARFAV----IVPDPAPAHNAAQDIPLVVAYEDEHLIVIDKPAGLVVHPAAGNPDGTLVNALLH-HCRGSLSGIGGVERPGIVHRIDKDTSGLMVAAKTDPAHVGLAAQFARHSIDRRYRAIVAGTPRLAAGTVDAPLAR-STADRKKIAIVADGRGKRAVTHYSVIEPLRRAALVECRLETGRTHQVRVHMASLGHPLLGDPVYGRSRPEHRELLNRLKFHRQALHAARLGFIHPVTSAALSFDSEIPQDMQD 311
>gi|118476866|ref|YP_894017.1| ribosomal large subunit pseudouridylate synthase D [Bacillus thuringiensis str. Al Hakam] >gi|196046511|ref|ZP_03113736.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus 03BB108] >gi|118416091|gb|ABK84510.1| ribosomal large subunit pseudouridylate synthase D [Bacillus thuringiensis str. Al Hakam] >gi|196022695|gb|EDX61377.1| ribosomal large subunit pseudouridine synthase, RluA family [Bacillus cereus 03BB108] (307 aa)
Score = 304, Expect = 5.5e-26, Identities = 81/246 (32%), Positives = 136/246 (55%)
  Q:    53 LKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKY--GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           L+    +EE   + P   ++++VYED ++LIVNKP  +  HP       TLAN++ + +  K     G   ++  +HRLDK T G V+ AK   +     +L +++KI++ Y AL+   ++ +   +DA I R    +T+R VS   D        +E  K +N TL  ++L TGRTHQIRVH  +  N ++ D +YG +     TKY   Q L A K+ F+HP T++E+ +++  P +  + +K++ +
  S:    66 LQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAFHYQMK-----GLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATKRRVSPKGDQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ-----TKYMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDTMKEFQR 304
>gi|183602394|ref|ZP_02963760.1| hypothetical protein BIFLAC_05095 [Bifidobacterium animalis subsp. lactis HN019] >gi|183218313|gb|EDT88958.1| hypothetical protein BIFLAC_05095 [Bifidobacterium animalis subsp. lactis HN019] (317 aa)
Score = 304, Expect = 5.7e-26, Identities = 90/290 (31%), Positives = 146/290 (50%)
  Q:     5 QRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNT-KVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPT-SYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R D+ V+    +SR+ A   IE     V G+ I K  T +  +  EI ++EE+   E     P   ++ I YED  I++V+KP  +  H +  +     L ++I+       I   G   R GIV RLD  T GL++V KS  ++    + F + +++K Y AL+  +L+     ++API R + S  R  +     KEA T +  + ++   TLA + L TGRTHQIRVH   I + ++ DP+YG  P+         Q+L A +L+F HP T     +    P + +  ++
  S:    14 KRFDVAVAKMMGISRAKATELIETGQARVIGRDIHKSATLQAGDTVEIDVREERREPE-----PVSNEMTIAYEDDDIVVVDKPVGVAAHASVGWTGPTVLGSLIQ---RGVHITSMGAAGRQGIVSRLDVGTSGLMLVCKSDLAYKEMRRQFSEHEVKKTYHALVQGNLKEDKATIEAPIGRAKVSDFR-FTVTPAGKEAVTHWDVMERFGEATLASINLETGRTHQIRVHFSSIGHPLVGDPMYGANPRLSQALGLERQWLHAMELEFRHPRTHINTVVTSRYPTDLQHALE 298
>gi|77358716|ref|YP_338280.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii RSA 493] >gi|71066706|gb|AAZ22628.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii RSA 493] (323 aa)
Score = 304, Expect = 5.7e-26, Identities = 97/289 (33%), Positives = 157/289 (54%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQT-RTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHIN-------KTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD +++  F   SRS  ++ I    V V+G   +K   KV E   I ++ +  +E  +   P    ++++YED+ +L++NKP  +IVHP +     TL N + +   S  +       R GI+HRLDK T GL+++A++L S +A  K    ++I ++Y A++   L + RT+E  AP+ R      R    +   + A T F+ I +Y+  T   V+L TGRTHQIRVH   I + +  DP+YG     P H++       KT K  Q L A  L+F HP  Q+ +  +  +P +    ++
  S:    20 RLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEAQ--LEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLSVV-----PRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIE--APVGRHPIHRTRMAVVEF-GRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKR-QALHAATLQFSHPVDQRPMACHAPLPADMAHLLE 311
>gi|15617005|ref|NP_240218.1| ribosomal large subunit pseudouridine synthase D [Buchnera aphidicola str. APS (Acyrthosiphon pisum)] >gi|11387080|sp|P57481|RLUD_BUCAI Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|25322332|pir||H84976 pseudouridylate synthase (EC 4.2.1.70) [imported] - Buchnera sp. (strain APS) >gi|10039070|dbj|BAB13104.1| ribosomal large subunit pseudouridine synthase D [Buchnera aphidicola str. APS (Acyrthosiphon pisum)] (312 aa)
Score = 304, Expect = 5.8e-26, Identities = 103/291 (35%), Positives = 160/291 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDI----------EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           QRLD+++S  F   SRS  K  I  N V VN  I+++P+ K+            +  ET  + P+ KD+          +IVYED  ILI+NKP  ++VHP S + S T+ N + Y + + K     D  R GIVHRLDK T GL+++AK++ S+N    L  ++KI ++Y  ++H  +      ++ PI R   + R  +      K + T +K ++++K  T   + L TGRTHQIRVH   IK  ++ DP Y            K  NK  K+  Q L A  L   HP  +  ++  + +P++ +E + K
  S:    18 QRLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKI------------LGGETLTIHPFSKDLLVDIPENIFLDIVYEDSDILIINKPAGLVVHPGSGNKSGTILNALLYHYKNSK-----DLPRAGIVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHGKMIAGGT-INKPIMR-HYNRRTCMMVHHLGKPSVTHYKVLSRFKFHTHIAIRLETGRTHQIRVHMLHIKYPLVGDPCYSGFKIQSNYRKDKKTNKIYKFPRQALHANHLSLHHPIKKNVMSWTVPLPQDIQELLLK 311
>gi|127513878|ref|YP_001095075.1| RluA family pseudouridine synthase [Shewanella loihica PV-4] >gi|126639173|gb|ABO24816.1| pseudouridine synthase, RluA family [Shewanella loihica PV-4] (323 aa)
Score = 304, Expect = 5.9e-26, Identities = 96/284 (33%), Positives = 153/284 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEI----ILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTK---------YGQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  ++  F   SR+  K  I+   V V+G + +KP  KV E  EI     LKEE   E   +      D++IVYED +I+++NK   ++VHP + +   TL N + +     ++       R GIVHRLDK T GL++VAK++++          ++I ++Y A++   +    V VD PI R  T  R  ++     + + T ++   K++  T   + L TGRTHQIRVH   I + ++ DP+YG  P+   K T            Q L A +L+  HPFT + ++    +P++
  S:    18 QRLDQTLAELFPDYSRTRIKEWIQAGAVYVDGMVQTKPREKVLEGQEIEIEATLKEEIKAEAQAI------DLDIVYEDDHIIVINKQAGLVVHPGAGNSDGTLMNALLHHCPEIELV-----PRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVSGTMTAGGV-VDEPIARHPTK-RTHMAVHHSGRPSVTHYRVAEKFRAHTRLRLRLETGRTHQIRVHMAHIGHILVGDPVYGGRPRPPKKATPELMEALNGFKRQALHAVRLELAHPFTCEIMSWQAPIPED 304
>gi|154249782|ref|YP_001410607.1| RluA family pseudouridine synthase [Fervidobacterium nodosum Rt17-B1] >gi|154153718|gb|ABS60950.1| pseudouridine synthase, RluA family [Fervidobacterium nodosum Rt17-B1] (314 aa)
Score = 304, Expect = 6.0e-26, Identities = 100/294 (34%), Positives = 158/294 (53%)
  Q:     2 KNTQRLDILVSSKFS--LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVET-STRREVSRDIDAKEARTIFKEINKYKNF-TLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +N  RLD  V  K    +SR+  +  I+N  V VNG    KP+ KV     I L   +  E  ++L P    ++I+YED+ IL++NK   II HP     S T+ N +  ++  K ++  G  LR GIVHRLDK T G++++AK+  +  + TK F D+  EK Y+ L+    + +  +++  I R      +  V+     K A T +K + ++ +   L      TGRTHQIRVH ++I + ++ D +YG    ++   +G   Q L A  L F HP T ++V     +P++FKE I+K
  S:     9 ENGWRLDKFVMEKTPEWISRTFIQRAIKNGEVLVNGTS-KKPSYKVKSGDIITLNAPEAPEIPEIL-PEDIPLDIIYEDRDILVINKQPGIITHPIPSHTSGTIVNGV--LYHCKDLQGIGGVLRPGIVHRLDKDTSGVMVIAKNDLAHQSLTKQFKDRLTEKLYICLVKGVPKRKEGDIEINIARNPVLRVKMTVTNSEYGKPALTHYKVVREFGDIAALVFAYPKTGRTHQIRVHMKYIGHPLMGDEVYGRAKEDEI--FGIKRQMLHALSLSFYHPRTGEKVKFIAKIPQDFKEAIQK 303
>gi|15640728|ref|NP_230358.1| 23S rRNA pseudouridine synthase D [Vibrio cholerae O1 biovar eltor str. N16961] >gi|153822744|ref|ZP_01975411.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae B33] >gi|194531595|ref|YP_002067044.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae MO10] >gi|34395835|sp|Q9KU20|RLUD_VIBCH Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|9655151|gb|AAF93874.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae O1 biovar El Tor str. N16961] >gi|125617549|gb|EAZ46111.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae MO10] >gi|126519727|gb|EAZ76950.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae B33] (324 aa)
Score = 304, Expect = 6.1e-26, Identities = 96/287 (33%), Positives = 153/287 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKD---IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKY------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           QRLD  V+  F+  SRS  K  +    + VNG +I+KP TKV    E+I  + ++ +E +    W+     + IVYED  I+++NKP D +VHP +     T+ N +  +F    I    +  R GIVHRLDK T GL++VAK++ +     +    + + ++Y A++   + T    +D PI R  ++ R  +S     K A T ++    ++  T   + L TGRTHQIRVH  ++++ ++ D  YG     PK   +           Q L A  LKF HP T +E+  +  +P +  E
  S:    18 QRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKV-MGGEVITVQAELEDEQR----WEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNAL--LFHYSPI---AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTM-TAGGMIDKPIGR-HSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGATEELTEMIRDFDRQALHAVMLKFEHPVTGEELEFHAPVPDDMVE 307
>gi|152971444|ref|YP_001336553.1| 23S rRNA pseudouridine synthase D [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] >gi|150956293|gb|ABR78323.1| 23S rRNA pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] (326 aa)
Score = 304, Expect = 6.4e-26, Identities = 99/290 (34%), Positives = 150/290 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +  V VNG I  KP  KV     I +  E  +EE     P    + IVYED  I+++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    V+ PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG     PK      I    K+  Q L A  L+  HP +  E+  +  +P++  E I+
  S:    18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGTIGDKPKEKVLGGERIAIDVE--IEEEARFQPQDIPLNIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHM-TAGGTVEEPISRHPTK-RTHMAVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMSHITHPLVGDQVYGGRPRPPKGASEEFITALRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
>gi|77972194|ref|ZP_00827768.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Yersinia frederiksenii ATCC 33641] (325 aa)
Score = 303, Expect = 6.5e-26, Identities = 96/289 (33%), Positives = 157/289 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKY---------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I ++ VTV+GK I+KP  KV    E++  + +I E+ +   P    ++IVYED  IL++NKP  ++VHP + +   T+ N + + +   KI    D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   ++ T    VD PI R  ++ R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG  P+     +            Q L A  L+  HP +  ++  +  +P++  E I
  S:    18 QRLDQALAELFPDYSRSRIKEWILDDRVTVDGKKINKPKEKV-LGGELVAIDAQIEEDAR-WAPQDIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYY--PKIM---DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNM-TAGGRVDEPISR-HSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFISILRGFDRQALHATMLRLYHPISGIQMEWHAALPEDMVELI 309
>gi|194681780|emb|CAR40996.1| ribosomal large subunit pseudouridine synthase D; ribosomal large subunit pseudouridine synthase d (ec 5.4.99.-) (rrna-uridine isomerase d) (rrna pseudouridylate synthase d) [Proteus mirabilis HI4320] (325 aa)
Score = 303, Expect = 6.9e-26, Identities = 97/290 (33%), Positives = 153/290 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG--PKHINKTTKY---------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           QRLD  ++  F   SRS  K  I +N V VN KII+KP  K+    +I  + + ++EE     P    + IVYED  IL++NKP D++VHP + +   T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+    +    + V+ PI R  T  R  ++     K A T ++ +  ++  T   + L TGRTHQIRVH   I + +I D +YG  P+ +   ++           Q L A  L+  HP T  E+  +  +P +  E I+
  S:    18 QRLDQALAELFPDYSRSRIKEWILDNRVQVNDKIINKPKEKMLGGEKI--EVDALIEEDVRWEPQNIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIV-----NVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVATGRMTAGGL-VNEPISRHPTK-RTHMAVHPMGKPAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHIHHPLIGDQLYGGRPRPLKGASEEFRETLRRFDRQALHATMLRLYHPITGIEMEWHAPLPDDMVELIR 310
>gi|91762258|ref|ZP_01264223.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1002] >gi|91718060|gb|EAS84710.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1002] (326 aa)
Score = 303, Expect = 7.1e-26, Identities = 97/289 (33%), Positives = 158/289 (54%)
  Q:     2 KNTQRLDILVSSKFSL-SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN-----FTLAEVELFTGRTHQIRVHAEFIKNHVIND---PIYGPKHINKTTKYG--------QYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +N  RLD+ ++ + +L SRS  K+ I    + +N +II+ P+ KV    EI L+  +  E +  L P+   ++IVYED  +LI+NKP  II+HP + +   T+ N + + ++   +   GD LR GIVHR+DK T GL+++AK+ ++    +  F +  I + Y  L+   L+  + ++D  I R   + +     +   K A T +K I  ++N      +L E  L TGRTHQIRVH   + N ++ D        K  N  T           Q+L A  L FIHP T +++     +P+E +
  S:    13 ENNLRLDVFINKRENLISRSRIKNLILKEKLKINDQIINSPSKKVLSGDEINLQIPEPKEAS--LKPYNFKLQIVYEDDDLLIINKPAGIIMHPGAGNYDETIVNALMH-YNKDSLSTIGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFSEHTITRVYQLLIWGKLRPSSGKIDTFITRSSKNRQMMEVSNSKGKRAITNYKTIEIFENDKTPTLSLVECRLETGRTHQIRVHMTHMGNSIMGDGKYKKKYKKLKNIDTNLENLIYKLDRQFLHAQTLGFIHPRTNEKMVFTSILPQELE 315
>gi|154705997|ref|YP_001424165.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii Dugway 5J108-111] >gi|154355283|gb|ABS76745.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii Dugway 5J108-111] (323 aa)
Score = 303, Expect = 7.3e-26, Identities = 97/289 (33%), Positives = 157/289 (54%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQT-RTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHIN-------KTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD +++  F   SRS  ++ I    V V+G   +K   KV E   I ++ +  +E  +   P    ++++YED+ +L++NKP  +IVHP +     TL N + +   S  +       R GI+HRLDK T GL+++A++L S +A  K    ++I ++Y A++   L + RT+E  AP+ R      R    +   + A T F+ I +Y+  T   V+L TGRTHQIRVH   I + +  DP+YG     P H++       KT K  Q L A  L+F HP  Q+ +  +  +P +    ++
  S:    20 RLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEAQ--LEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLSVV-----PRAGIIHRLDKDTSGLLLIARTLASHHALIKTMKARQIVREYEAIVKGVLISGRTIE--APVGRHPIHRTRMAVVEF-GRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKR-QALHAATLQFSHPVDQRPMACHAPLPADMAHLLE 311
>gi|78186656|ref|YP_374699.1| pseudouridine synthase, RluD [Pelodictyon luteolum DSM 273] >gi|78166558|gb|ABB23656.1| ribosomal large subunit pseudouridine synthase D [Pelodictyon luteolum DSM 273] (354 aa)
Score = 303, Expect = 7.5e-26, Identities = 88/278 (31%), Positives = 144/278 (51%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN---FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---------------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +R+  +  IE+  V VNGK + K N +V     I +   +       L P    I+IVYED  +++VNK   ++VHP   + + TLAN I + F +   +   D LR GIVHRLDK T GL+IVA++  + +   + F D+K+ K Y A+L    + +   +   I R     +   +   +  E +T   +    +N   F+LAE+ L TGRTHQIR H + + + ++ D  YG   + +T  +                Q L A  L F  P T + ++    +P++  + ++K
  S:    52 TRNKVQEAIEDGRVLVNGKSV-KSNYRVKSCDSIEMTFLR--PPAPELAPEDIPIDIVYEDSDLMVVNKAPGMVVHPAFGNWTGTLANAILHHFGTDAEELETDELRPGIVHRLDKDTSGLIIVARNPTALHRLARQFADRKVSKLYTAILWGVPEPQEGTIHTNIGRSRRDRKVMANFPYEGLEGKTAITDYRVTENLHWFSLAELTLHTGRTHQIRAHMQHLGHQILGDTTYGGASL-RTLDFPRSESFVKNLLDLLPRQALHAASLSFHQPTTGRPLSFTAPLPEDMAQALEK 343
>gi|15605391|ref|NP_220177.1| ribosomal large subunit pseudouridine synthase D [Chlamydia trachomatis D/UW-3/CX] >gi|3329108|gb|AAC68253.1| Pseudouridine Synthase [Chlamydia trachomatis D/UW-3/CX] (334 aa)
Score = 303, Expect = 7.5e-26, Identities = 98/292 (33%), Positives = 158/292 (54%)
  Q:     4 TQRLDI-LVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHN-----HLQTRTVEVDAPIKRVET---STRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           T RLD  LVS   + SR+  + +IE   V VNG++ ++ +  +    +++  E    EE   L P    ++ VYED  +L++NKP D++VHP       T+ + ++  I +  K ++  +P R GIVHRLDK T GL+I  K+  +   +++LF  ++++K Y+A+  N      + TR      P+KR E    ST  E       KEA T  + +      ++  +   TGRTHQ+RVH + +   ++ DP+YG   IN   +YG   Q L AY L F HP + + V +   +P +    I+K
  S:    20 TGRLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPL-SLGDVVEVELIEEEEPSSLIPEDIPLDKVYEDDMMLVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQERIHTRIAR--HPLKRKEMTVLSTHAE-----GGKEAITHCQVLATNGRLSVVALYPETGRTHQLRVHMKHLGTPILGDPVYGIPSIN--FRYGLDKQQLHAYSLVFAHPESAERVKLVTKLPDDMTSLIEK 314
>gi|88806703|ref|ZP_01122219.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea biformata HTCC2501] >gi|88783037|gb|EAR14210.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea biformata HTCC2501] (343 aa)
Score = 303, Expect = 7.5e-26, Identities = 80/233 (34%), Positives = 128/233 (54%)
  Q:    64 VLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRD-IDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           +L P    ++IVYED+ +L+VNKP  ++VHP   + + TL N + +  D   +  +  P   G+VHR+DK T GL+++AK+  +     + F D+   ++YLAL+  ++   +  V+ PI R  +   + +V  D    KEA T ++   +    TL    L TGRTHQIRVH + I + + ND  YG   I K T + +Y               L A  L F HP + KE++    +P++    I K+
  S:    88 LLLPEDIPLDIVYEDEVLLVVNKPAGMVVHPGHGNYTGTLVNALVHHLDQLPLNSDNRP---GLVHRIDKETSGLLVIAKTEAAMANLARQFFDKTTRREYLALVWGNVADDSGTVEGPIGRNPKNRLQMQVFPDGSQGKEAVTHYRVEERLGYVTLVSCRLETGRTHQIRVHMQHIGHTIFNDSRYGGDRILKGTSFTKYKQFVENAFKILPRQALHARTLGFTHPLSGKELDFEAPVPEDMAACIIKW 334
>gi|121587761|ref|ZP_01677521.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae 2740-80] >gi|121730333|ref|ZP_01682696.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae V52] >gi|147673459|ref|YP_001216201.1| 23S rRNA pseudouridine synthase D [Vibrio cholerae O395] >gi|153215116|ref|ZP_01949823.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae 1587] >gi|153801880|ref|ZP_01956466.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae MZO-3] >gi|153818725|ref|ZP_01971392.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae NCTC 8457] >gi|153826766|ref|ZP_01979433.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae MZO-2] >gi|153829371|ref|ZP_01982038.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae 623-39] >gi|194534998|ref|YP_002070189.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae RC385] >gi|194537757|ref|YP_002072896.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae V51] >gi|121547988|gb|EAX58068.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae 2740-80] >gi|121627915|gb|EAX60491.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae V52] >gi|124114907|gb|EAY33727.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae 1587] >gi|124122591|gb|EAY41334.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae MZO-3] >gi|125622370|gb|EAZ50690.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae V51] >gi|126510747|gb|EAZ73341.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae NCTC 8457] >gi|146315342|gb|ABQ19881.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae O395] >gi|148875154|gb|EDL73289.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae 623-39] >gi|149739417|gb|EDM53657.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae MZO-2] >gi|150419792|gb|EDN12107.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae RC385] >gi|150422124|gb|EDN14091.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae AM-19226] (324 aa)
Score = 303, Expect = 7.7e-26, Identities = 96/287 (33%), Positives = 153/287 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKD---IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKY------GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKE 291
           QRLD  V+  F+  SRS  K  +    + VNG +I+KP TKV    E+I  + ++ +E +    W+     + IVYED  I+++NKP D +VHP +     T+ N +  +F    I    +  R GIVHRLDK T GL++VAK++ +     +    + + ++Y A++   + T    +D PI R  ++ R  +S     K A T ++    ++  T   + L TGRTHQIRVH  ++++ ++ D  YG     PK   +           Q L A  LKF HP T +E+  +  +P +  E
  S:    18 QRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKV-MGGEVITVQAELEDEQR----WEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNAL--LFHYPPI---AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTM-TAGGMIDKPIGR-HSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGATEELTEMIRDFDRQALHAVMLKFEHPVTGEELEFHAPVPDDMVE 307
>gi|89075039|ref|ZP_01161480.1| putative ribosomal large subunit pseudouridine synthase D [Photobacterium sp. SKA34] >gi|89049126|gb|EAR54691.1| putative ribosomal large subunit pseudouridine synthase D [Photobacterium sp. SKA34] (324 aa)
Score = 303, Expect = 7.9e-26, Identities = 91/281 (32%), Positives = 150/281 (53%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMP 286
           RLD +++  +   SRS  K  I N +V+VNG ++ KP  K+    E+ ++ E  +E+          ++IVYED  IL++NKP D +VHP +     T+ N + +   S       +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y AL    + T    ++ PI R  ++ R  ++     K+A T ++   +++  T   + L TGRTHQIRVH  ++ + +I D IYG          P+ I     +  Q L A  L+  HP T +++  +  +P
  S:    19 RLDQVIAQLYPDYSRSRIKDWILNGMVSVNGDVVKKPREKMMGGEELFIQAE--IEDEVRWVAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTILNALLHYCPSL-----AEVPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEALAIGQM-TGGGTIEKPIGR-HSTKRICMAVHEMGKDAITHYRVAERFREHTRIVLRLETGRTHQIRVHMSYMSHPLIGDVIYGGRPRPPRDASPEFIQALRAFDRQALHARMLRLDHPITGEKMEWHAPLP 302
>gi|163750158|ref|ZP_02157401.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA) [Shewanella benthica KT99] >gi|161330215|gb|EDQ01197.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA) [Shewanella benthica KT99] (324 aa)
Score = 303, Expect = 7.9e-26, Identities = 96/284 (33%), Positives = 156/284 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKY--------GQYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  ++  F   SR+  K  I +  VT++G + +KP  KV E  EI +    +VEET        D+ IVYED +IL++NK   ++VHP + +   TL N + +     ++       R GIVHRLDK T GL++VAK++++          ++I ++Y A++   L +    VD PI R  T  R  ++  +  K A T F+   K++  T   + L +GRTHQIRVH   + + ++ DP+YG     PK +  T ++         Q L A +L+  HP+T + ++    +P++
  S:    18 QRLDQTLAELFPDYSRTRIKEWILDGSVTIDGNVSNKPREKVLEGQEIEVGA-TLVEETTA-KAQAIDLNIVYEDDHILVINKQAGLVVHPGAGNSDGTLLNALLHHCPGIELV-----PRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAIVMGSLISGGT-VDEPIDRHPTK-RTHMAVVLSGKPAMTHFRVAEKFRAHTRLRLRLESGRTHQIRVHMAHLGHTLVGDPVYGGRPRPPKAV--TPEFFEIFMGFKRQALHAIRLELAHPYTCEIMSWQAPVPED 304
>gi|74316828|ref|YP_314568.1| ribosomal large subunit pseudouridine synthase D [Thiobacillus denitrificans ATCC 25259] >gi|74056323|gb|AAZ96763.1| pseudouridine synthase, RluD [Thiobacillus denitrificans ATCC 25259] (318 aa)
Score = 303, Expect = 8.2e-26, Identities = 76/223 (34%), Positives = 123/223 (55%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHIN--KTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +++VYED  +L++NKP  ++VHP S +   TL N + +     ++    +  R GIVHRLDK T GL++VAK+L +     +    + ++++YLAL++  +  R   VDAP+ R     T+R V      KEA T +  + ++   TL   +L TGRTHQIRVH + + + ++ D +Y     +  K     Q L A KL  IHP T + V+    +P +F   ++
  S:    91 LDVVYEDSMLLVINKPVGLVVHPGSGNRDGTLLNALLH-----RVPQVAELPRAGIVHRLDKDTSGLLVVAKTLRAHTDLVRQLQARTVKREYLALVYGEVD-RGGTVDAPLARDPHNRTKRTVHSL--GKEAVTHYDVVERFPGITLLRCKLETGRTHQIRVHMQHVGHPLVGDTVYSASRRSHLKIPFPRQALHAEKLGLIHPVTGEFVHWECPLPPDFGSLLQ 308
>gi|145633599|ref|ZP_01789327.1| SfhB [Haemophilus influenzae 3655] >gi|144985805|gb|EDJ92419.1| SfhB [Haemophilus influenzae 3655] (324 aa)
Score = 303, Expect = 8.3e-26, Identities = 98/289 (33%), Positives = 155/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYGQYLVAYK--------LKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  IE +LV +N +I + P  KV   E  EII++    VE+          + IVYED  I+++NKP D++VHP + + + T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+   VD P+ R   + R  ++     K A T ++ +  Y+N+T   + L TGRTHQIRVH   I + ++ D  YG     PK  N +  + + L  +K        L+  HP T + +     +P +F E +
  S:    17 QRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE----VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI-----AEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASG-IMTKGGTVDQPMAR-HATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPK--NASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308
>gi|42629156|ref|ZP_00154705.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Haemophilus influenzae R2846] (324 aa)
Score = 302, Expect = 8.4e-26, Identities = 98/289 (33%), Positives = 155/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYGQYLVAYK--------LKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  IE +LV +N +I + P  KV   E  EII++    VE+          + IVYED  I+++NKP D++VHP + + + T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+   VD P+ R   + R  ++     K A T ++ +  Y+N+T   + L TGRTHQIRVH   I + ++ D  YG     PK  N +  + + L  +K        L+  HP T + +     +P +F E +
  S:    17 QRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE----VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIS-----EVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASG-IMTKGGTVDQPMAR-HATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPK--NASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308
>gi|94497522|ref|ZP_01304091.1| Pseudouridine synthase, RluD [Sphingomonas sp. SKA58] >gi|94422939|gb|EAT07971.1| Pseudouridine synthase, RluD [Sphingomonas sp. SKA58] (317 aa)
Score = 302, Expect = 8.5e-26, Identities = 77/222 (34%), Positives = 123/222 (55%)
  Q:    72 IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRR-EVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGP-----KHINKTTKY-GQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           + IV+ED  +L+V+KP  ++VHP + +L  TL N + +   + ++   G   R GIVHR+DK T GL++VAK+  +     + F D  IE+ Y A+ +         VD+ I R +   ++  V R+   K A T ++ +++ +   L E  L TGRTHQ+RVH   I + +I DP+YG      K I +T  +  Q L A  L FIHP T + +     +P + +E +
  S:    85 LTIVHEDADLLVVDKPAGLVVHPAAGNLDGTLVNALLH-HCAGQLSGIGGVARPGIVHRIDKDTSGLLVVAKTDRAHEGLARQFKDHSIERAYAAITYGIPVPPAGTVDSWIGRSDADRKKMAVHREGRGKHAVTHYRTLDRLRGAALVECRLETGRTHQVRVHMAHIGHPLIGDPVYGRERKGFKSILETLGFRRQALHARMLGFIHPVTDEPLMFESALPADVQELL 312
>gi|168212841|ref|ZP_02638466.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE str. F4969] >gi|170715523|gb|EDT27705.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE str. F4969] (298 aa)
Score = 302, Expect = 8.6e-26, Identities = 94/293 (32%), Positives = 153/293 (52%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + +++   +  +  LS  + +    +  + V+G +  K N  V    EI ++  K  +E++ + P K DIEIVYED  IL++NK   ++VHPT    + TLAN I Y F     K +     + +V RLD  T GL+I+ K+  +    +      K +K+YLA++H +L+ +   ++ PI R    T + V  D   +E+ T +K I  Y    L E  L TGRTHQIRVH   + + +  D +YG +     ++  Q L AY L F  P T++ +++  D+P++ KE I K
  S:    13 DKRKIREFLKEELGLSSRLIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSK--KESQNIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYF-----KESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISR--QALHAYGLDFYSPKTKEPLSLRADLPEDMKELINK 294
>gi|148825561|ref|YP_001290314.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae PittEE] >gi|148715721|gb|ABQ97931.1| SfhB [Haemophilus influenzae PittEE] (324 aa)
Score = 302, Expect = 8.7e-26, Identities = 98/289 (33%), Positives = 155/289 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYGQYLVAYK--------LKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  IE +LV +N +I + P  KV   E  EII++    VE+          + IVYED  I+++NKP D++VHP + + + T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+   VD P+ R   + R  ++     K A T ++ +  Y+N+T   + L TGRTHQIRVH   I + ++ D  YG     PK  N +  + + L  +K        L+  HP T + +     +P +F E +
  S:    17 QRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE----VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI-----AEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASG-IMTKGGTVDQPMDR-HATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPK--NASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308
>gi|167855786|ref|ZP_02478539.1| ribosomal large subunit pseudouridine synthase D [Haemophilus parasuis 29755] >gi|167853065|gb|EDS24326.1| ribosomal large subunit pseudouridine synthase D [Haemophilus parasuis 29755] (325 aa)
Score = 302, Expect = 9.0e-26, Identities = 95/289 (32%), Positives = 157/289 (54%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLV-----------AYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD  ++  F   SRS  K  IE++LV+VNGKI++K   KV      +++ +  +EE     P    + IVYED  IL++NKP D++VHP + +   T+ N + + +         +  R GIVHRLDK T GL++VAK++ +          ++I ++Y A+    + T+  +VD P+ R  T  R  ++     K A T ++ + +++N+T   + L TGRTHQIRVH   I + ++ D +YG +        G++L            A  L+  HP T + +  +  +P +F E I+
  S:    19 RLDQALAQLFPDYSRSRIKVWIESDLVSVNGKIVNKAREKV--FGGELIEIQAEIEEEIRFEPQNIPLNIVYEDDDILVINKPKDLVVHPGAGNPDGTVLNALLHHYPQI-----AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVTALQKREITREYEAVASG-IMTQGGKVDEPMARHPTK-RTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGRPRPPKGASGEFLEVLRNFKRQALHATMLRLHHPITGELMEWHAPLPDDFVELIE 310
>gi|49475182|ref|YP_033223.1| ribosomal large subunit pseudouridine synthase D [Bartonella henselae str. Houston-1] >gi|49237987|emb|CAF27192.1| Ribosomal large subunit pseudouridine synthase D [Bartonella henselae str. Houston-1] (334 aa)
Score = 302, Expect = 9.1e-26, Identities = 97/294 (32%), Positives = 160/294 (54%)
  Q:     5 QRLDILVSSKFS--LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIE---------IVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQ----KIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREV---SRDIDAKEARTIFKEINKYKN-------FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG------------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYGK 298
           QRLD  ++ ++   LSRS  +  I    + V+G++I +P TK        LK  +I+E T    P  +D E         I++ED +++++NKP  ++VHP + + + TL N + +    K +   G   R GIVHRLDK T G+++VAK+  +  + +  F D      ++++Y AL+          +DAP+ R   +  ++    ++ + A+ A T F  + +Y          +L E  L TGRTHQIRVH   I + ++ D +YG     K+                Q L A  L F HP T K ++ +  +P++  E IK   K
  S:    14 QRLDQWLAKQYHNVLSRSRLQALIREGYLKVDGQLIKEPKTK--------LKSNQIIELT---MPALRDAEPSGEAIALDILFEDDHVIVINKPAGLVVHPGNGNWTGTLVNALIH-HCGKSLSGIGGVKRPGIVHRLDKNTSGVMVVAKNDLAHKSLSAQFFDHGRTSALDRRYHALIWGSPNRNVWTIDAPVGRSPHNRTKQAVVYNQCLHARHAVTHFSLLEQYGTCADKTPFASLLECRLETGRTHQIRVHMAHIGHPLVGDTVYGNAFKTKSNTLNSIIKNAIDQFNRQALHAANLTFEHPATGKIMSFSSPLPQDMAELIKHLKK 332
>gi|91227645|ref|ZP_01261922.1| ribosomal large subunit pseudouridine synthase D [Vibrio alginolyticus 12G01] >gi|91188424|gb|EAS74718.1| ribosomal large subunit pseudouridine synthase D [Vibrio alginolyticus 12G01] (325 aa)
Score = 302, Expect = 9.2e-26, Identities = 91/284 (32%), Positives = 154/284 (54%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG-----------QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  ++  F+  SRS  K  + +  V V+G++++KP TKV    EI L+ E  +E+ +        ++IVYED+ I+++NKP D +VHP +     T+ N + + + D  ++       R GIVHRLDK T GL++VAK++ +     +    + I ++Y A+    + T   +VD PI R  ++ R  ++     K A T ++   +++  T   + L TGRTHQIRVH  ++++ ++ D  YG +    T               Q L A  L+F HP T + +  +  +P +
  S:    18 QRLDQAIAELFADFSRSRLKEWLLDGKVQVDGEVVTKPRTKVMGGEEITLQAE--LEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAEVP------RAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRM-TAGGKVDQPIGR-HSTKRTLMAVAPMGKPAVTHYRVAERFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPTGASEELTAMIRGFDRQALHAVMLRFEHPITGEVLEFHAPVPDD 304
>gi|56478105|ref|YP_159694.1| ribosomal large subunit pseudouridine synthase D [Azoarcus sp. EbN1] >gi|56314148|emb|CAI08793.1| ribosomal large subunit pseudouridine synthase D [Azoarcus sp. EbN1] (306 aa)
Score = 302, Expect = 9.5e-26, Identities = 77/217 (35%), Positives = 122/217 (56%)
  Q:    74 IVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETS-TRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +V+ED+ IL+++KP  ++VHP S + S TL N + +       +    P R GIVHRLDK T GL++VAK+L+S  A  +    + + + YLAL+H  +    + V+API R  T  TR  V +    + A T ++   ++   TL E +L TGRTHQIRVH  +I + ++ D  YG +            Q L A++L  +HP +  E+     +P++F+
  S:    82 VVHEDEEILVIDKPVGLVVHPGSGNWSGTLLNALLH----HAPQLAAVP-RAGIVHRLDKDTSGLLVVAKTLESQTALVRQLQARTVRRHYLALVHRAVAGAGM-VEAPIGRHPTQRTRMAVVQ--SGRAAVTRYRPRERFARVTLVECQLETGRTHQIRVHMAYIGHPLVGDATYGLRRSGSPVLDAFARQALHAFRLGLLHPASGAEMTWESPLPEDFE 294
>gi|86358939|ref|YP_470831.1| pseudouridylate synthase, ribosomal large subunit D protein [Rhizobium etli CFN 42] >gi|86283041|gb|ABC92104.1| pseudouridylate synthase, ribosomal large subunit D protein [Rhizobium etli CFN 42] (354 aa)
Score = 302, Expect = 9.7e-26, Identities = 102/283 (36%), Positives = 163/283 (57%)
  Q:     6 RLDILVSSKF--SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDI--EIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPL-------RMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQ----KIEKKYLALLHNHLQTRTVEVDAPIKRVETS-TRREVSR--DIDAKEARTIFKEINKYKN-------FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTK-YG-QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           RLD  ++++     SRS  K  I++  V++ G+ ++ P  KV   +  EI L E +        TP  +DI  EI++ED  +++++KP  ++VHP S + + TL N +        I + GD L       R GIVHRLDK T G+++VAK+  +    +  F D      +E+ Y A++    +T +  +DAP+ R     TRR V R    DA  A T ++ I +++         +L E  L TGRTHQIRVH   I + ++ D +YG          P+ I K    +G Q L A+ L+F HP T + ++  + +P +
  S:    37 RLDAWLTAQVGEDFSRSRIKALIKDGQVSLRGEQVTDPQRKVRVGDSFEITLPEPEDP------TPKGEDIPLEILHEDDDLIVISKPAGLVVHPGSGNWTGTLVNAL--------IHHCGDTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYRAVVWGRPRTLSGTIDAPLGRATGDRTRRAVKRPDSQDADAAITHYEVIERFQENPDATALASLVECHLETGRTHQIRVHMAHIGHPLVGDTVYGAGFRTKANLLPEEIRKVVNGFGRQALHAFMLQFEHPRTGELMHFEVPLPDD 344
>gi|163846479|ref|YP_001634523.1| RluA family pseudouridine synthase [Chloroflexus aurantiacus J-10-fl] >gi|187602981|ref|ZP_02989202.1| pseudouridine synthase, RluA family [Chloroflexus sp. Y-400-fl] >gi|172045876|sp|Q45826|Y901_CHLAA Uncharacterized RNA pseudouridine synthase Caur_0901 (RNA-uridine isomerase) (RNA pseudouridylate synthase) >gi|163667768|gb|ABY34134.1| pseudouridine synthase, RluA family [Chloroflexus aurantiacus J-10-fl] >gi|187484879|gb|EDU22859.1| pseudouridine synthase, RluA family [Chloroflexus sp. Y-400-fl] (316 aa)
Score = 302, Expect = 9.8e-26, Identities = 87/294 (29%), Positives = 149/294 (50%)
  Q:     2 KNTQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK----HINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           +  +R+D  L  +   LSR+  +  IE   V  +G+   + +  V   + I L     +    V  P   D+  VYED  I ++NKP  ++VHP       TL N +   +    I   G  LR GIVHRLD+ T GL+++A+   +  +       +++ K Y AL+       T  +DAPI R +   R  ++   D + ART ++ ++ + +++L EV+L TGRTHQIRVH   +   ++ DP+YGP+    H+++     Q+L A  L  +HP + +       +P + +  +++
  S:    23 QTAERIDRFLAGAMPDLSRAQVQRLIEQGFVLYDGRS-PRASQPVRPGAVIQLTIPPPIPTELVAEPIPLDV--VYEDADIAVINKPAGMVVHPAPGHPRGTLVNALLARYPDLAI---GGELRPGIVHRLDRDTSGLLVIARHDQAMRSLVDQQQARRMRKIYQALVIGR-PPETGTIDAPIGR-DPRDRLRMAVVPDGRPARTHYRLLDTFGDYSLLEVQLETGRTHQIRVHLRHLGYPIVGDPVYGPRRSHLHLSR-----QFLHAAYLGLVHPRSGRWQEFTAPLPADLQIVLRQ 308
>gi|88713056|ref|ZP_01107140.1| ribosomal large subunit pseudouridine synthase D [Flavobacteriales bacterium HTCC2170] >gi|88708437|gb|EAR00673.1| ribosomal large subunit pseudouridine synthase D [Flavobacteriales bacterium HTCC2170] (341 aa)
Score = 302, Expect = 9.9e-26, Identities = 91/279 (32%), Positives = 154/279 (55%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVS---RDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           +R+  +   ++  + VN KI+ K N KV    E+ +  E    E  +LTP    ++IVYED  +L+VNKP  ++VHP   + + TL N +  ++ SK +  N +  R G+VHR+DK T GL++VAK+  +     K F D+  E++Y+AL+  +++  +  ++  I R     R ++         KEA T +  + +    TL   +L TGRTHQIRVH ++I + + ND  YG   + K T + +Y               L A  L F+HP + + +  + ++P++    I K+
  S:    43 TRNKIQQAAKDGHIWVNEKIV-KQNYKVKAGDEVKVLFEHPPYEL-LLTPENIPLDIVYEDDVLLVVNKPAGMVVHPGHGNYTGTLINAL--LYHSKDLPVNSND-RPGLVHRIDKDTSGLLVVAKTEAAMTHLAKQFFDKTSEREYVALVWGNVEDESGTIEGNIAR-NPKNRLQMQVFPEGEQGKEAVTHYGVLERLGYVTLVSCKLETGRTHQIRVHMKYIGHTLFNDERYGGDKVLKGTTFTKYKQFVDNAFKILPRQALHAKTLGFVHPVSGEMMRFDSEIPEDMSLCIDKW 333
>gi|145620418|ref|ZP_01776449.1| pseudouridine synthase, RluA family [Geobacter bemidjiensis Bem] >gi|144943243|gb|EDJ78337.1| pseudouridine synthase, RluA family [Geobacter bemidjiensis Bem] >gi|197089120|gb|ACH40391.1| pseudouridine synthase, RluA family [Geobacter bemidjiensis Bem] (319 aa)
Score = 302, Expect = 1.0e-25, Identities = 92/286 (32%), Positives = 148/286 (51%)
  Q:     3 NTQRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG----------PKHINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           + +RLD  +S     L+RS A   IE    TVNG    KP  K+   E  ++++      E      P    IE++YED  +++VNK   ++VHP + +   TL N +  +   K +   G  LR GIVHR+DK T G ++VAK   + NA  + F +  I++ YLAL++   +     +++ I R  T  ++  ++    K+A T ++ + +Y   TL  + L TGRTHQIRVH     + ++ D +YG          P         G Q L A  L F+HP + K +  + ++P +
  S:    13 DPERLDSFISRSVPELTRSAALRLIETGFATVNGSK-QKPALKLKGGEVVQVVVPPPTPAEPQPEEIP----IEVLYEDAELVVVNKGAGMVVHPGAGNPEGTLVNAL--LAHCKDLSGIGGELRPGIVHRIDKDTSGTLVVAKCDRAHNALAEQFKEHSIKRVYLALVYGSPKEDKGRIESTIGRHPTDRKKMSAKARHGKQAVTHWRVVARYPGITLIRLRLETGRTHQIRVHMSEAGHPLLADEVYGGTGRLSGVQDPVLKQMIKSMGRQALHAKTLGFLHPVSGKYLEFDTELPPD 305
>gi|126666670|ref|ZP_01737647.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp. ELB17] >gi|126628715|gb|EAZ99335.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp. ELB17] (325 aa)
Score = 302, Expect = 1.0e-25, Identities = 92/273 (33%), Positives = 151/273 (55%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKD---IEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           SRS  +  +++  +TVNG    KP  KV    ++ L  E   + T     W+ +   ++IVYED++ILI+NKP  ++VHP +     TL N I  I    +     +  R GIVHRLDK T G+++VA+SL +  +       + + ++Y A++   L T    VDAPI R  T  R+ ++     K A T ++ I ++   T    +L +GRTHQIRVH   +K+ ++ DP+YG     PK   +  +      + Q L A +L   HP T + ++ ++ +P++F+
  S:    34 SRSRLQSWVKSGALTVNGGQ-CKPRDKVMLGDKLELDAEPEAQVT-----WQAEAITLDIVYEDEHILIINKPAGLVVHPAAGHADGTLVNAILNIAPEVE-----NLPRAGIVHRLDKDTSGVMVVARSLIAHTSLVNQLQTRTMGREYEAVVVGTL-TGGATVDAPIGRHPTE-RKRMAVVKSGKPAVTHYRVIERFSAHTHVRCKLESGRTHQIRVHLTHVKHPLVGDPVYGGRLRLPKGTTEELREVLSGFHRQALHARQLTLEHPQTGETMSWDVPLPEDFQ 307
>gi|167619842|ref|ZP_02388473.1| ribosomal large subunit pseudouridine synthase D [Burkholderia thailandensis Bt4] (385 aa)
Score = 302, Expect = 1.1e-25, Identities = 92/293 (31%), Positives = 150/293 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD  ++  F   SRS  +  IE+  V V+G   +K    V   + I L  + ++ E    TP    + IVYED  I++V+KP  ++VHP + + S TL N + + +        G P R GIVHRLDK T GL++VA++L +     +    + ++++Y AL+   +      +DAPI R     TR  V      K ART F+ ++    + +  +    +L TGRTHQIRVH   + + ++ DP+YG     ++          Q L A++L  +HP T + +     +P +    +   G
  S:    58 ERLDKALAQLFPEFSRSRLQQWIESERVRVDGAP-AKIRQAVPLGATIELLPD-LLPEQLAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAA----GLP-RAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDEGT-IDAPIGRDPRERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPATGRSMQWRAPLPADLAALVDALG 354
>gi|167581726|ref|ZP_02374600.1| ribosomal large subunit pseudouridine synthase D [Burkholderia thailandensis TXDOH] (389 aa)
Score = 302, Expect = 1.1e-25, Identities = 92/293 (31%), Positives = 150/293 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD  ++  F   SRS  +  IE+  V V+G   +K    V   + I L  + ++ E    TP    + IVYED  I++V+KP  ++VHP + + S TL N + + +        G P R GIVHRLDK T GL++VA++L +     +    + ++++Y AL+   +      +DAPI R     TR  V      K ART F+ ++    + +  +    +L TGRTHQIRVH   + + ++ DP+YG     ++          Q L A++L  +HP T + +     +P +    +   G
  S:    62 ERLDKALAQLFPEFSRSRLQQWIESERVRVDGAP-AKIRQAVPLGATIELLPD-LLPEQLAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAA----GLP-RAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDEGT-IDAPIGRDPRERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPATGRSMQWRAPLPADLAALVDALG 358
>gi|83719070|ref|YP_442774.1| ribosomal large subunit pseudouridine synthase D [Burkholderia thailandensis E264] >gi|83652895|gb|ABC36958.1| ribosomal large subunit pseudouridine synthase D [Burkholderia thailandensis E264] (391 aa)
Score = 302, Expect = 1.1e-25, Identities = 92/293 (31%), Positives = 150/293 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD  ++  F   SRS  +  IE+  V V+G   +K    V   + I L  + ++ E    TP    + IVYED  I++V+KP  ++VHP + + S TL N + + +        G P R GIVHRLDK T GL++VA++L +     +    + ++++Y AL+   +      +DAPI R     TR  V      K ART F+ ++    + +  +    +L TGRTHQIRVH   + + ++ DP+YG     ++          Q L A++L  +HP T + +     +P +    +   G
  S:    64 ERLDKALAQLFPEFSRSRLQQWIESERVRVDGAP-AKIRQAVPLGATIELLPD-LLPEQLAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAA----GLP-RAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDEGT-IDAPIGRDPRERTRMAVVTGAAGKPARTHFRTVDTTPWERQPVSAIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPATGRSMQWRAPLPADLAALVDALG 360
>gi|194538682|ref|YP_002073756.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25] >gi|151937237|gb|EDN56104.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25] (325 aa)
Score = 302, Expect = 1.1e-25, Identities = 91/284 (32%), Positives = 153/284 (53%)
  Q:     5 QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIF-DSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG-----------QYLVAYKLKFIHPFTQKEVNINLDMPKE 288
           QRLD  ++  F+  SRS  K  + +  V VNG++++KP TKV    EI L+ E  +E+ +        ++IV+ED  I+++NKP D +VHP +     T+ N + + + D  ++       R GIVHRLDK T GL++VAK++ +     +    + I ++Y A+    + T   +VD PI R  ++ R  ++     K A T ++   +++  T   + L TGRTHQIRVH  ++++ ++ D  YG +    T               Q L A  L+F HP T + +  +  +P +
  S:    18 QRLDQAIAELFADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEITLQAE--LEDEERWEAQDIPLDIVFEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAEVP------RAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRM-TAGGKVDQPIGR-HSTKRTLMAVAPMGKPAVTHYRVAERFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPTGASEELTAMIRGFDRQALHAVMLRFEHPITGEVLEFHAPVPDD 304
>gi|76789398|ref|YP_328484.1| ribosomal large subunit pseudouridine synthase D [Chlamydia trachomatis A/HAR-13] >gi|76167928|gb|AAX50936.1| ribosomal large subunit pseudouridine synthase D [Chlamydia trachomatis A/HAR-13] (335 aa)
Score = 301, Expect = 1.2e-25, Identities = 99/292 (33%), Positives = 157/292 (53%)
  Q:     4 TQRLDI-LVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNH-----LQTRTVEVDAPIKRVET---STRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           T RLD  LVS   + SR+  + +IE   V VNG++ ++ +  +    +++  E    EE   L P    ++ VYED  IL++NKP D++VHP       T+ + ++  I +  K ++  +P R GIVHRLDK T GL+I  K+  +   +++LF  ++++K Y+A+  N      + TR      P+KR E    ST  E       KEA T    +      ++  +   TGRTHQ+RVH + +   ++ DP+YG   IN   +YG   Q L AY L F HP + + V +   +P +    I+K
  S:    21 TGRLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPL-SLGDVVEVELIEEEEPSSLIPEDIPLDKVYEDDMILVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQELIHTRIAR--HPLKRKEMTVLSTHAE-----GGKEAITHCHVLATNGRLSVVALYPETGRTHQLRVHMKHLGTPILGDPVYGIPSIN--FRYGLDKQQLHAYSLVFAHPESAERVKLVTKLPDDMTSLIEK 315
>gi|190575601|ref|YP_001973446.1| putative ribosomal large subunit pseudouridine synthase D [Stenotrophomonas maltophilia K279a] >gi|190013523|emb|CAQ47158.1| putative ribosomal large subunit pseudouridine synthase D [Stenotrophomonas maltophilia K279a] (329 aa)
Score = 301, Expect = 1.2e-25, Identities = 93/290 (32%), Positives = 154/290 (53%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKV-LTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           +R D +V+  F   SRS     I+   V ++G  + +P   +     + L    +V ET+    P    +++++ED+++L++NKP  ++VHP + + S TL N + +   S  +     P R GIVHRLDK T G+++VAK+L++  A  +    + + ++YLA++   L       DAPI R      +   R+ D KEA T ++   +++  T  E  L TGRTHQIRVH   +++ +I DP+YG     PK  +            Q L A  L+F HP T + V     +P++    +K
  S:    21 RRFDAVVAELFPEYSRSRLTEWIKAGEVLLDGAQV-RPRDPLRGGEVVTLN---VVLETQTDAQPEDIPLDVLFEDEHLLVINKPVGLVVHPGAGNHSGTLVNALLFRDPSVAVL----P-RAGIVHRLDKDTSGVMVVAKTLEAQTALVEQLAARDVHRQYLAIVMGALVAGGT-ADAPIDRHPRDRLKMAVRE-DGKEAITHYRLRERFRAHTALECRLETGRTHQIRVHMAHVRHPIIGDPLYGGALKLPKGASDELVAALRGFKRQALHAETLEFTHPITGELVRNTAPVPEDMLHLMK 312
>gi|168205929|ref|ZP_02631934.1| pseudouridine synthase, RluA family [Clostridium perfringens E str. JGS1987] >gi|170662629|gb|EDT15312.1| pseudouridine synthase, RluA family [Clostridium perfringens E str. JGS1987] (298 aa)
Score = 301, Expect = 1.2e-25, Identities = 94/293 (32%), Positives = 152/293 (51%)
  Q:     3 NTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           + +++   +  +  LS  + +    +  + V+G +  K N  V    EI ++  K  +E++ + P K DIEIVYED  IL++NK   ++VHPT    + TLAN I Y F     K +     + +V RLD  T GL+I+ K+  +    +      K +K+YLA++H +L  +   ++ PI R    T + V  D   +E+ T +K I  Y    L E  L TGRTHQIRVH   + + +  D +YG +     ++  Q L AY L F  P T++ +++  D+P++ KE I K
  S:    13 DKRKIREFLKEELGLSSRLIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSK--KESQNIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYF-----KESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLAEKEGTINRPIYRPAEDTIKRVV-DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISR--QALHAYGLDFYSPKTKEPLSLRADLPEDMKELINK 294
>gi|107029027|ref|YP_626122.1| pseudouridine synthase, RluD [Burkholderia cenocepacia AU 1054] >gi|116689814|ref|YP_835437.1| RluA family pseudouridine synthase [Burkholderia cenocepacia HI2424] >gi|194559073|ref|YP_002094100.1| Pseudouridine synthase, RluD [Burkholderia cenocepacia PC184] >gi|105898191|gb|ABF81149.1| ribosomal large subunit pseudouridine synthase D [Burkholderia cenocepacia AU 1054] >gi|116647903|gb|ABK08544.1| ribosomal large subunit pseudouridine synthase D [Burkholderia cenocepacia HI2424] >gi|124872864|gb|EAY64580.1| Pseudouridine synthase, RluD [Burkholderia cenocepacia PC184] (402 aa)
Score = 301, Expect = 1.2e-25, Identities = 89/293 (30%), Positives = 151/293 (51%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEIN----KYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTK------YGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKYG 297
           +RLD  ++  F   SRS  +  IE   V V+G   +K    V   ++I L  + ++ E    TP    ++++YED  ++++NKP  ++VHP + + S T+ N + + +        G P R GIVHRLDK T GL++VA++L +     +    + ++++Y AL+   +      +DAPI R     TR  V      K ART F+ ++    + +  +  + +L TGRTHQIRVH     + ++ DP+YG     ++          Q L A++L  +HP T K +     +P +    +   G
  S:    69 ERLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAP-AKIRQPVPLGAKIALVPD-LLPEQLAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAA---GLP-RAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEEGT-IDAPIGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGLVHPVTGKAMQWRCPLPDDMNTLVAALG 366
>gi|153209393|ref|ZP_01947379.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii 'MSU Goat Q177'] >gi|120575364|gb|EAX31988.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii 'MSU Goat Q177'] (323 aa)
Score = 301, Expect = 1.3e-25, Identities = 96/289 (33%), Positives = 156/289 (53%)
  Q:     6 RLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQT-RTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHIN-------KTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIK 294
           RLD +++  F   SRS  ++ I    V V+G   +K   KV E   I ++ +  +E  +   P    ++++YED+ +L++NKP  +IVHP +     TL N + +   S  +       R GI+HRLDK T GL+++A++L S +A  K    ++I ++Y A++   L + RT+E  AP+ R      R    +   + A T F+ I +Y+  T   V+L TGRTHQIRVH   I + +  DP+YG     P H++       KT K  Q L    L+F HP  Q+ +  +  +P +    ++
  S:    20 RLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEAQ--LEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLSVV-----PRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIE--APVGRHPIHRTRMAVVEF-GRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKR-QALHGATLQFSHPVDQRPMACHAPLPADMAHLLE 311
>gi|16761516|ref|NP_457133.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Typhi str. CT18] >gi|16765978|ref|NP_461593.1| 23S rRNA pseudouridine synthase D [Salmonella typhimurium LT2] >gi|29142987|ref|NP_806329.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Typhi str. Ty2] >gi|62181235|ref|YP_217652.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67] >gi|167545942|ref|ZP_02341509.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Saintpaul str. SARA23] >gi|167553892|ref|ZP_02347635.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Saintpaul str. SARA29] >gi|167559988|ref|ZP_02352993.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853] >gi|167992440|ref|ZP_02573538.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. CVM23701] >gi|168218963|ref|ZP_02644195.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Agona str. SL483] >gi|168227812|ref|ZP_02653043.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Javiana str. GA_MM04042433] >gi|168234182|ref|ZP_02659240.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Kentucky str. CDC 191] >gi|168239430|ref|ZP_02664488.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Schwarzengrund str. SL480] >gi|168244683|ref|ZP_02669615.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Heidelberg str. SL486] >gi|168262167|ref|ZP_02684140.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Hadar str. RI_05P066] >gi|168464166|ref|ZP_02698083.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Newport str. SL317] >gi|168478390|ref|ZP_02707413.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Virchow str. SL491] >gi|168822474|ref|ZP_02834474.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Weltevreden str. HI_N05-537] >gi|194446496|ref|YP_002041926.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Newport str. SL254] >gi|194447791|ref|YP_002046668.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Heidelberg str. SL476] >gi|194471474|ref|ZP_03077458.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188] >gi|194737121|ref|YP_002115673.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633] >gi|54039251|sp|P65837|RLUD_SALTI Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|54041742|sp|P65836|RLUD_SALTY Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|25322403|pir||AC0832 pseudouridylate synthase (EC 4.2.1.70) - Salmonella enterica subsp. enterica serovar Typhi (strain CT18) >gi|16421209|gb|AAL21552.1| pseudouridine synthase [Salmonella typhimurium LT2] >gi|16503817|emb|CAD05842.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica serovar Typhi] >gi|29138619|gb|AAO70189.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica serovar Typhi Ty2] >gi|62128868|gb|AAX66571.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA) [Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67] >gi|194405159|gb|ACF65381.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Newport str. SL254] >gi|194406095|gb|ACF66314.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Heidelberg str. SL476] >gi|194457838|gb|EDX46677.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188] >gi|194712623|gb|ACF91844.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633] >gi|195633435|gb|EDX51849.1| ribosomal large subunit pseudouridine synthase D [Salmonella enterica subsp. enterica serovar Newport str. SL317] (326 aa)
Score = 301, Expect = 1.3e-25, Identities = 97/289 (33%), Positives = 151/289 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PK-----HINKTTKYG-QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  I N  V VNG++  KP  KV     + +  E  ++E          ++IVYED  IL++NKP D++VHP + +   T+ N + + +         D  R GIVHRLDK T GL++VAK++ +     +    ++I ++Y A+   H+ T    V+ PI R  T  R  +S     K A T ++ +  ++  T   + L TGRTHQIRVH   I + ++ D +YG     PK      I+   K+  Q L A  L+  HP +  E+  +  +P++  + I
  S:    18 QRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDAE--IDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHM-TAGGTVNEPISRHPTK-RTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPVSGIEMEWHAPIPQDMVDLI 309
>gi|32423742|gb|AAP81266.1| pseudouridine synthase [Pseudomonas aeruginosa] (320 aa)
Score = 301, Expect = 1.3e-25, Identities = 94/285 (32%), Positives = 154/285 (54%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY-IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDA-KEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYG------QYLVAYKLKFIHPFTQKEVNINLDMPKEF 289
           QRLD + +  F   SRS     I++  +TV+G ++ +P   V   ++++L+ E+  E          ++EIVYED++IL+++KP  ++VHP +     TL N + Y + D   +       R GIVHRLDK T GL++VAK+L++          + + + Y A++   + T    +DAPI R     +R+    +DA K A + ++ + +++  T   V+L TGRTHQIRVH   I   ++ DP+YG     P   ++T          Q L A  L+  HP T   +     +P+EF
  S:    18 QRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVL-RPRDIVHSGAQLVLEAEQ--EAQGEWLAQDIELEIVYEDEHILVIDKPAGLVVHPAAGHQDGTLLNALLYHVPDIANVP------RAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGVI-TSGGTIDAPIGR--HGVQRQKMAVVDAGKVAVSHYRVLERFRAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGRFRIPPVASQTLVQTLREFPRQALHARFLELDHPATGVRMKWESPLPEEF 304
>gi|166154000|ref|YP_001654118.1| ribosomal large subunit pseudouridine synthase D [Chlamydia trachomatis 434/Bu] >gi|166154875|ref|YP_001653130.1| ribosomal large subunit pseudouridine synthase D [Chlamydia trachomatis L2b/UCH-1/proctitis] >gi|165929988|emb|CAP03471.1| ribosomal large subunit pseudouridine synthase D [Chlamydia trachomatis 434/Bu] >gi|165930863|emb|CAP06425.1| ribosomal large subunit pseudouridine synthase D [Chlamydia trachomatis L2b/UCH-1/proctitis] (335 aa)
Score = 301, Expect = 1.4e-25, Identities = 99/292 (33%), Positives = 157/292 (53%)
  Q:     4 TQRLDI-LVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLAN-IIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNH-----LQTRTVEVDAPIKRVET---STRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKK 295
           T RLD  LVS   + SR+  + +IE   V VNG++ ++ +  +    +++  E    EE   L P    ++ VYED  IL++NKP D++VHP       T+ + ++  I +  K ++  +P R GIVHRLDK T GL+I  K+  +   +++LF  ++++K Y+A+  N      + TR      P+KR E    ST  E       KEA T    +      ++  +   TGRTHQ+RVH + +   ++ DP+YG   IN   +YG   Q L AY L F HP + + V +   +P +    I+K
  S:    21 TGRLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPL-SLGDVVEVELIEEEEPSSLIPEDIPLDKVYEDDMILVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQELIHTRITR--HPLKRKEMTVLSTHAE-----GGKEAITHCHVLATNGRLSVVALYPETGRTHQLRVHMKHLGTPILGDPVYGIPSIN--FRYGLDKQQLHAYSLVFAHPESAERVKLVTKLPDDMTSLIEK 315
>gi|152990499|ref|YP_001356221.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp. SB155-2] >gi|151422360|dbj|BAF69864.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp. SB155-2] (319 aa)
Score = 301, Expect = 1.4e-25, Identities = 93/295 (31%), Positives = 159/295 (53%)
  Q:     2 KNTQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEES--EIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKN--FTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           +  +RLD  ++ K    R+  +  I+   V +NGKI  K  +K+      E+ + E K+ +   V      D+E +YED+ IL++NKP  ++VHP       TL + +K   D      +G+  R GIVHRLDK T GL+++AK+ ++  A +K   D+ + + YLA++   L+   + ++ PI R     R ++      + A++ F ++   KN  + L   +LFTGRTHQIRVH   I  H++ D +YG K  + T     +L AY L   HP + +++     +P++  ++++KY
  S:     9 REKERLDKALAKKLQKPRNQIEQLIKQGYVRINGKIEKKAGSKLKSGDLVEVTIPEPKVSQPKDV----HFDVERIYEDEDILVLNKPAGLVVHPAPSVKEPTLVDWLK-ANDISLSTLSGEE-RHGIVHRLDKETSGLIVIAKNNETHQALSKQLQDKSMGRYYLAIVEPPLKEDLI-IEKPIAR-NPKNRLKMGVVEGGRYAKSAFVKLTTSKNNKYELIGAKLFTGRTHQIRVHLASINRHILGDSLYGFKSKSVTIPR-VFLHAYILYLKHPKSGEKMRFLAPVPEDMLDFLQKY 298
>gi|189464334|ref|ZP_03013119.1| hypothetical protein BACINT_00675 [Bacteroides intestinalis DSM 17393] >gi|189438124|gb|EDV07109.1| hypothetical protein BACINT_00675 [Bacteroides intestinalis DSM 17393] (357 aa)
Score = 301, Expect = 1.4e-25, Identities = 91/279 (32%), Positives = 144/279 (51%)
  Q:    18 SRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKR-VETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQY---------------LVAYKLKFIHPFTQKEVNINLDMPKEFKEYIKKY 296
           SR+  +   E   V  N K + K + KV     I +  ++   E +V+ P    + IVYEDKY++IVNKP  ++VHP   +   TL N I +        Y+ +   +G+VHR+DK T GL+++AK+ D+       F ++  +++Y AL+   ++     +   I R  +   +  V  D   K A T ++ + +    TL E  L TGRTHQIRVH + I + + ND  YG   I K T + +Y               L A  L F+HP T +E+    +MP +  + I K+
  S:    56 SRNRIQKSAEAGFVMANNKPV-KSSYKVKPMDVITIMMDRPRYENEVI-PEDIPLNIVYEDKYLMIVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNP-DYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRRYRALVWGIVEQDEGTIIGNIGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQALHAMTLGFVHPATGEEMYFTSEMPDDMTQLIDKW 347
>gi|145641509|ref|ZP_01797087.1| SfhB [Haemophilus influenzae R3021] >gi|145273800|gb|EDK13668.1| SfhB [Haemophilus influenzae 22.4-21] (324 aa)
Score = 301, Expect = 1.4e-25, Identities = 99/289 (34%), Positives = 153/289 (52%)
  Q:     5 QRLDILVSSKF-SLSRSIAKHKIENNLVTVNGKIISKPNTKV--DEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYG-----PKHINKTTKYGQYLVAYK--------LKFIHPFTQKEVNINLDMPKEFKEYI 293
           QRLD  ++  F   SRS  K  IE +LV +N +I + P  KV   E  EII++    VE+          + IVYED  I+++NKP D++VHP + + + T+ N + Y +         +  R GIVHRLDK T GL++VAK++ +     +    +KI ++Y A+    + T+   VD P+ R  T         I  K A T ++ +  Y+N+T   + L TGRTHQIRVH   I + ++ D  YG     PK  N +  + + L  +K        L+  HP T + +     +P +F E +
  S:    17 QRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE----VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIS-----EVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASG-IMTKGGTVDQPMARHATKRTLMAVHPI-GKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPK--NASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308
>gi|124267192|ref|YP_001021196.1| ribosomal large subunit pseudouridine synthase D [Methylibium petroleiphilum PM1] >gi|124259967|gb|ABM94961.1| ribosomal large subunit pseudouridine synthase D [Methylibium petroleiphilum PM1] (334 aa)
Score = 300, Expect = 1.5e-25, Identities = 85/286 (29%), Positives = 149/286 (52%)
  Q:     5 QRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVD--EESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQYLVAYKLKFIHPFTQKEVNINLDMPKEFK 290
           +RLD  L +     SR+  +  IE   V ++G+ ++    +V   ++ EI L       E++   P    + +V+ED ++L+++KP  ++VHP   + S T+ N +     +        P R GIVHRLDK T GL++VAK+L +  +  +    +++ ++YLAL+H  L+     VDAPI R +  +R +++     + ART  + I      +     L TGRTHQIRVH     + ++ D +YG +     T+  Q L A++L F+HP + + +  +   P + +
  S:    33 ERLDRWLATLAGEFSRNHLQTLIEGGQVRIDGQTVTARARRVSAGQQIEITLLP---TPESQAFRPEPVALPVVFEDAHLLVIDKPAGLVVHPAPGNWSGTVLNGLL----AHHAGAAALP-RAGIVHRLDKDTSGLMVVAKTLPAMTSLVRAIAAREVHREYLALVHGVLRQAVFSVDAPIGR-DPVSRIKMAVLAGGRTARTDVELIAARDAVSAVRCTLHTGRTHQIRVHMASRGHALLADALYGGRPGLGLTR--QALHAHRLGFVHPASLQPIEFSAVPPDDLR 310
>gi|118047866|ref|ZP_01516492.1| Pseudouridine synthase, RluD [Chloroflexus aggregans DSM 9485] >gi|117995615|gb|EAV09830.1| Pseudouridine synthase, RluD [Chloroflexus aggregans DSM 9485] (310 aa)
Score = 300, Expect = 1.5e-25, Identities = 90/269 (33%), Positives = 142/269 (52%)
  Q:     5 QRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIIS-----KPNTKVDEESEIILKEEKIVEETKVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPK--HINKTTKYGQYLVAYKLKFIHP 273
           QR+D  L +S   LSR+  +  IE  +V   G+         P T +     + +     VE    L P    ++IVYED  + ++NKP  ++VHP       TL N +   +    I  +G+ +R GIVHRLD+ T GL+++A+   +  A  +    +++ K Y AL+          +DAPI R +   R  ++   D + ART ++ I  + +++L EV+L TGRTHQIRVH   +   ++ DP+YGP+  H+  T    Q+L A +L F HP
  S:    26 QRIDRFLAASMPDLSRTQVQRLIEQGMVLYAGRPTRASQPLHPGTII----HVTIPPPVPVE----LMPESIPLDIVYEDADVAVINKPAGMVVHPAPGHPRGTLVNALLARYPDLAI--SGE-VRPGIVHRLDRDTSGLLVIARHDAALRALVEQQQARRMRKIYQALVVGRPPV-CGTIDAPIGR-DPRDRLRMAVVADGRPARTHYRVIATFGDYSLLEVQLETGRTHQIRVHLRHLGYPIVGDPVYGPRRSHLRLTR---QFLHAGQLGFFHP 286