>gi|26553465|ref|NP_757399.1| pseudouridine synthase [Mycoplasma penetrans HF-2] >gi|26453471|dbj|BAC43803.1| pseudouridine synthase [Mycoplasma penetrans HF-2] (301 aa)
Score = 1295, Expect = 7.6e-141, Identities = 301/301 (100%), Positives = 301/301 (100%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKFK 301
           MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKFK
  S:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKFK 301
>gi|160934208|ref|ZP_02081595.1| hypothetical protein CLOLEP_03079 [Clostridium leptum DSM 753] >gi|156866881|gb|EDO60253.1| hypothetical protein CLOLEP_03079 [Clostridium leptum DSM 753] (319 aa)
Score = 480, Expect = 2.1e-46, Identities = 117/300 (39%), Positives = 189/300 (63%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKE-LKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEK-----KDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEID-RENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN---FGFQFPCLTSYKIKFNFDKNH-FLHYLNKLNLEVKNIKF 300
           M QI + K +  Q L  F++K++ +L  S + K I+  +IK+N K+   + ++QE D + ++L+ +  ++   + +FL+A  +++ +YED+NI+++NK  GL+  PD+N   D+L  R++ YLYEK     +++N     L +R+D+ T+G+ +AAKN + L  LN+      + KYYLC+ +GK +KKSD L  ++  NE K  + I  R     K I TKYR ++QK+  +LLE+ LLTG+ HQIR HMASIGHP++GD KY K        +++  L SYK+ F+F  +   L+YLN     V  + F
  S:     1 MRQITVGKNDAGQRLDKFLTKTYTKLPQSMLYKGIRTKNIKLNGKRCQISSRIQEGDIISLYLKEEFFEQTPTEYDFLKAPKVVDCVYEDENILLLNKKPGLLVHPDENYHFDSLIARVQHYLYEKGEYQPQNENSFAPALVNRIDRNTSGIVIAAKNAEALRILNDKMRKRELHKYYLCVVHGKMEKKSDLLVGYLEKNESKNRVYISARPFPGAKTIQTKYRTLQQKEKYSLLEVDLLTGRTHQIRAHMASIGHPLVGDGKYGKNTQNRESRYKWQALCSYKLVFDFQTDAGILNYLNHREFTVPQVWF 311
>gi|167771608|ref|ZP_02443661.1| hypothetical protein ANACOL_02980 [Anaerotruncus colihominis DSM 17241] >gi|167666248|gb|EDS10378.1| hypothetical protein ANACOL_02980 [Anaerotruncus colihominis DSM 17241] (338 aa)
Score = 463, Expect = 2.0e-44, Identities = 109/301 (36%), Positives = 175/301 (58%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPI-KKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE-----KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN---FGFQFPCLTSYKIKFNFDKNH-FLHYLNKLNLEVKNIKFK 301
           M +  I   +  Q +  F++K+   L  S + K+I+   IK+N K+   + +L   D L ++L       ++   +FL +   +++IYED+NI++VNKP GL+   D+++  DTL NRI+ +LY        ++N     LC+R+D+ T G+ +AAKN   L  LN       + K YLC+ +G   K+SDTLK F+  +     + + D      + I+T YRV+ QK  ++LLEI LLTG+ HQIR H+A IGHP+LGD KY +  +    G +   L +YK+ F+F  +   L+ LN  + EV ++ F+
  S:    18 MREFQINGNDAGQRVDKFLTKAVPLLPQSMLYKAIRTKRIKLNGKRCEISTRLCTGDQLTLYLNDSFFDSRDGAFSFLRSPAAIDIIYEDENILLVNKPAGLVVHEDEHQSSDTLINRIQHHLYNCGVYNPAEENSFAPALCNRIDRNTAGIVIAAKNAAALRILNEKIKARELQKLYLCIVHGTMPKESDTLKAFLRKDARTNTVAVYDHPIPDGRTILTHYRVVAQKDRLSLLEIDLLTGRTHQIRAHLAHIGHPLLGDAKYGRNRDNHKTGLKHQALCAYKLTFHFQSDAGVLNGLNGRSFEVLDVWFR 329
>gi|13357670|ref|NP_077944.1| pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum serovar 3 str. ATCC 700970] >gi|170762339|ref|YP_001752196.1| pseudouridine synthase [Ureaplasma parvum serovar 3 str. ATCC 27815] >gi|171920337|ref|ZP_02691044.2| pseudouridine synthase [Ureaplasma parvum serovar 1 str. ATCC 27813] >gi|183508769|ref|ZP_02689887.2| pseudouridine synthase [Ureaplasma parvum serovar 14 str. ATCC 33697] >gi|186701771|ref|ZP_02553233.2| pseudouridine synthase [Ureaplasma parvum serovar 6 str. ATCC 27818] >gi|11357016|pir||C82933 pseudouridine synthase (uracil hydrolase) UU113 [imported] - Ureaplasma urealyticum >gi|6899069|gb|AAF30519.1|AE002111_8 pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum serovar 3 str. ATCC 700970] >gi|168827916|gb|ACA33178.1| pseudouridine synthase [Ureaplasma parvum serovar 3 str. ATCC 27815] >gi|171902761|gb|EDT49050.1| pseudouridine synthase [Ureaplasma parvum serovar 1 str. ATCC 27813] >gi|182675707|gb|EDT87612.1| pseudouridine synthase [Ureaplasma parvum serovar 14 str. ATCC 33697] >gi|186701046|gb|EDU19328.1| pseudouridine synthase [Ureaplasma parvum serovar 6 str. ATCC 27818] (315 aa)
Score = 444, Expect = 3.7e-42, Identities = 125/298 (41%), Positives = 181/298 (60%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKK-----DKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG---NFGFQFPCLTSYKIKF-NFDKNHF--LHYLNKLNLEVKNIKF 300
           +I IK  + NQ L  F+ K+F  LS   + K I+  D+KVNHKK   NY L+END + I+ +   ++K++ L+F  AK  L++IYEDKNI+VV+KP GLI   D   K DTL NRIKKYL +K      D++    +LCHRLD  T+GL VAAK    L  +  ++    V + Y CL Y +  K +D + +F++  ++  ++  + + KFNK  ITKY  I++ K   + +I+LLTG+ HQIR  +  +  P++G+ KY  K    N  + + CL SYKIKF N  K     L+YL      +KNI F
  S:     5 EIKIKINDANQRLDRFLLKNFPNLSRIAVYKIIRTKDVKVNHKKVDHNYLLKENDVVSIYAKENFLEKKVDLSFANAKDELDIIYEDKNILVVHKPIGLIVHEDNRYKNDTLQNRIKKYLVKKDEYHPFDESAFVPSLCHRLDLNTSGLIVAAKTANALRVITEMFKNNDVIRIYKCLTYNQLPKNNDVIYNFMYKADDNTMIVQNFKTKFNKTAITKYTYIDKYKKYFIYDIELLTGRTHQIRAVLNFLHAPIVGEQKYITKDIDKNQNYMYQCLVSYKIKFINLKKYQCEELNYLENKEFRIKNIWF 313
>gi|185178732|ref|ZP_02554745.2| pseudouridine synthase [Ureaplasma urealyticum serovar 5 str. ATCC 27817] >gi|188024269|ref|ZP_02569983.2| pseudouridine synthase [Ureaplasma urealyticum serovar 7 str. ATCC 27819] >gi|188039360|ref|ZP_02528207.2| pseudouridine synthase [Ureaplasma urealyticum serovar 8] >gi|188518686|ref|ZP_02557148.2| pseudouridine synthase [Ureaplasma urealyticum serovar 11 str. ATCC 33695] >gi|188592546|ref|ZP_02694127.2| pseudouridine synthase [Ureaplasma urealyticum serovar 10] >gi|184209334|gb|EDU06377.1| pseudouridine synthase [Ureaplasma urealyticum serovar 5 str. ATCC 27817] >gi|188018935|gb|EDU56975.1| pseudouridine synthase [Ureaplasma urealyticum serovar 7 str. ATCC 27819] >gi|188997684|gb|EDU66781.1| pseudouridine synthase [Ureaplasma urealyticum serovar 11 str. ATCC 33695] (315 aa)
Score = 432, Expect = 7.7e-41, Identities = 116/275 (42%), Positives = 169/275 (61%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKK-----DKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG---NFGFQFPCLTSYKIKF 277
           +I IK  + NQ L  F+ K+F  LS   I K I+  DIKVNHKK   NY L+END + I+ +   ++K++ L+F +AK  L +IYED NI+VV+KP GLI   D N K DTL NRIKKYL +K      D++    +LCHRLD  T+GL VAAK    L  +  ++    V++ Y CL Y +  K +D + ++++   +  ++  + + K NK  ITKY+ I   K   + +I+LLTG+ HQIR  +  +  P++G+ KY  K    N  +++ CL SYKIKF
  S:     5 EIKIKINDANQRLDRFLLKNFPNLSRIAIYKLIRTKDIKVNHKKAEHNYLLKENDVVSIYAKENFLEKKIDLDFAKAKDELEIIYEDSNILVVHKPIGLIVHEDDNHKNDTLQNRIKKYLVKKNEYHPFDESAFVPSLCHRLDLNTSGLIVAAKTANALRIIAEMFKNNDVNRVYKCLTYNRLPKNNDIVYNYMYKANDNTMIVQNFKTKVNKTAITKYQYIGNYKKYFVYDIELLTGRTHQIRAVLNFLHAPIVGEQKYITKDIDKNQNYEYQCLVSYKIKF 287
>gi|171920745|ref|ZP_02695367.2| pseudouridine synthase [Ureaplasma urealyticum serovar 13 str. ATCC 33698] >gi|188524118|ref|ZP_02557392.2| pseudouridine synthase [Ureaplasma urealyticum serovar 12 str. ATCC 33696] >gi|188531087|ref|ZP_02547198.2| pseudouridine synthase [Ureaplasma urealyticum serovar 4 str. ATCC 27816] >gi|188568732|ref|ZP_02828795.2| pseudouridine synthase [Ureaplasma urealyticum serovar 2] >gi|195867425|ref|ZP_03079429.1| pseudouridine synthase [Ureaplasma urealyticum serovar 9 str. ATCC 33175] >gi|171903495|gb|EDT49784.1| pseudouridine synthase [Ureaplasma urealyticum serovar 13 str. ATCC 33698] >gi|195659776|gb|EDX53156.1| pseudouridine synthase [Ureaplasma urealyticum serovar 12 str. ATCC 33696] >gi|195660901|gb|EDX54154.1| pseudouridine synthase [Ureaplasma urealyticum serovar 9 str. ATCC 33175] (315 aa)
Score = 432, Expect = 7.8e-41, Identities = 116/275 (42%), Positives = 169/275 (61%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKK-----DKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG---NFGFQFPCLTSYKIKF 277
           +I IK  + NQ L  F+ K+F  LS   I K I+  DIKVNHKK   NY L+END + I+ +   ++K++ L+F +AK  L +IYED NI+VV+KP GLI   D N K DTL NRIKKYL +K      D++    +LCHRLD  T+GL VAAK    L  +  ++    V++ Y CL Y +  K +D + ++++   +  ++  + + K NK  ITKY+ I   K   + +I+LLTG+ HQIR  +  +  P++G+ KY  K    N  +++ CL SYKIKF
  S:     5 EIKIKINDANQRLDRFLLKNFPNLSRIAIYKLIRTKDIKVNHKKAEHNYLLKENDVVSIYAKENFLEKKIDLDFAKAKDELEIIYEDSNILVVHKPIGLIVHEDDNHKNDTLQNRIKKYLVKKNEYHPFDESAFVPSLCHRLDLNTSGLIVAAKTANALRIIAEMFKNNDVNRVYKCLTYNRLPKNNDIVYNYMYKANDNTMIVQNFKTKVNKTAITKYQYIGNYKKYFVYDIELLTGRTHQIRAVLNFLHAPIVGEQKYITKDIDKNQNYEYQCLVSYKIKF 287
>gi|167750591|ref|ZP_02422718.1| hypothetical protein EUBSIR_01567 [Eubacterium siraeum DSM 15702] >gi|167656517|gb|EDS00647.1| hypothetical protein EUBSIR_01567 [Eubacterium siraeum DSM 15702] (322 aa)
Score = 414, Expect = 1.1e-38, Identities = 111/279 (39%), Positives = 171/279 (61%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFL---RLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEK---KDKNYLE--ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY-NKKGN--FGFQFPCLTSYKIKFNF 279
           M +I + K +  Q +  F+SKSF  L   +I K  +   IK+N KK   +  + END +++F+    L P  K    +F      ++++YED+NI++V+KP G++   D++   DTL NRIK YLY K   + +N L     LC+R+D+ T G+ +AAKN ++L  LN       ++K YLC+  GK    S TL  ++  N +   ++I D++ K N  I TKY+VI    + +LL++ LLTG+ HQIR H+A IGH +LGD KY N K N  +GF++  L SY+++F F
  S:     1 MKEIKVTKNDSGQRIDRFLSKSFP-LGQGQICKLARKNCIKLNGKKCKPDTHIAENDIIKLFIPDEMLIPKAKSDPDDFTAVSDKIDIVYEDENILLVDKPVGMVVHEDESGDSDTLINRIKSYLYHKGEYRPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKIRDRELTKLYLCIACGKVTPDSATLTAYLEKNSDTNTVKISDKKTKSNLTIKTKYKVIAYNGENSLLKVDLLTGRTHQIRAHLAYIGHALLGDGKYGNNKLNKKYGFKYQALCSYELQFKF 290
>gi|160915826|ref|ZP_02078034.1| hypothetical protein EUBDOL_01842 [Eubacterium dolichum DSM 3991] >gi|158432302|gb|EDP10591.1| hypothetical protein EUBDOL_01842 [Eubacterium dolichum DSM 3991] (313 aa)
Score = 407, Expect = 6.3e-38, Identities = 101/298 (33%), Positives = 166/298 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNI 298
           M +I I K + +Q +  F+SK+   L  S + K+I+N  IKVN K+   + +LQE D++Q+FL  +    ++   FL+    L+++YED+N+++VNK +GL+   D+    D L +RI  YLY  K+     +N     LCHR+D+ T GL +AAKN  +L  +N       V K Y+C+  G F K+ + +  +    ++     +    +  K I   Y++ EQKK  AL+E++LL+GK HQIR  +A + HP+ GD KY  K      +  L +Y+I+F + +   L  +    +E+  I
  S:     1 MREIVIGKNDCDQRVDKFLSKALPTLPKSLMYKAIRNKKIKVNRKRCEISQRLQEGDTMQLFLAEEFFMTQIDTAFLKVPSELDIVYEDENLLIVNKAKGLLAHRDQKVGQDNLMDRILHYLYIHKEYDPRMENSFVPALCHRIDRNTQGLVIAAKNAASLRAMNAHIKQRKVRKKYVCIAQGVFDKRQEHVLLYHCKTKDNVAHILPYPKEGYKPIEINYQIKEQKKQYALVEVELLSGKSHQIRAMLAYLSHPLYGDVKYGAKHTAAKHYQMLCAYRIEFVWKQEDVLANMRGRVIELDKI 303
>gi|154498138|ref|ZP_02036516.1| hypothetical protein BACCAP_02119 [Bacteroides capillosus ATCC 29799] >gi|150273128|gb|EDN00285.1| hypothetical protein BACCAP_02119 [Bacteroides capillosus ATCC 29799] (321 aa)
Score = 397, Expect = 1.0e-36, Identities = 99/279 (35%), Positives = 162/279 (58%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKK-ELKLNFLEA-KPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN---FG-FQFPCLTSYKIKFNF 279
           M +  IKK +  Q L  ++ K+   L      K I+   +KVN K +  +Y+LQE D LQ+++  +      L+  FL   KP LN++YED+N+++V+K  G++  PD+ E+++TL   I+ YLY+KK+     +N     LC+R+D+ T G+ +AAKN +TL  +N       + K+YL +  GK       L+ F+  +E +KQ+          +  +T Y+ ++    ++L+E +LLTG+ HQIR   A  GHP+LGD KY ++ +   FG      L SYK+ F+F
  S:     1 MKEFTIKKNDAGQRLDRWLGKTLPLLPAPLAQKYIRLKRVKVNGKGSARDYRLQEGDFLQLYINDEFFDTPTLENAFLSVFKPRLNIVYEDENLLLVDKQPGIVVHPDETERVNTLITHIQAYLYQKKEWSPYKENSFAPALCNRIDRNTGGIVIAAKNAETLRIMNQKIKDREIDKFYLAVVLGKMNPPEGRLEGFLVKDEVKKQVTVYHHPVPDGRTALTVYKTLKVGNGLSLVECELLTGRTHQIRAQFADAGHPLLGDGKYGRERDNRRFGRTNGQALYSYKLTFSF 291
>gi|31544701|ref|NP_853279.1| hypothetical protein MGA_0186 [Mycoplasma gallisepticum R] >gi|31541547|gb|AAP56847.1| RluA [Mycoplasma gallisepticum R] (330 aa)
Score = 378, Expect = 1.4e-34, Identities = 109/294 (37%), Positives = 177/294 (60%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLIC-QPDKNEKIDTLNNRIKKYLYEKKDKNYLE-----ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRE-NKFNKEIITKYRVIE--QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------GNFGFQFPCLTSYKIKF---NFDKNHFLHYLNKLNLEVKN 297
           I IK  ++   +  F+ K  K  + + I K I+  DI VN+++  ++Y L+ ND +  +  L+   K+    F +AKP L++IYED+N+++  KP G+   Q D+  + D + NR+  YL +    +YL       ++ +RLD YTTG+ + AKN K    LN +     + K+Y CL +G+   K  TL  ++  +  + ++ I +E    NK IIT+Y+ +   +K++  LL+++L+TG+ HQIR H+ASI HPV+GD KY KK      GNF  Q   L SYKI F   N+D++  L YL++   + K+
  S:     5 IVIKSVDDCIRIDKFLFKYLKNYTRTNIYKMIRKKDITVNNQRIDFDYILKVNDKITYYDFLRTDHKKKVPEFFKAKPELDLIYEDENLVIFEKPLGIPAQQTDEPSQYDHMQNRLVHYLVKSNQYDYLNNQAYLPSIVNRLDTYTTGIMLGAKNLKAQQALNQIIKNRDLKKFYHCLVHGEINPKKATLTAYLTKDPNRSLVSIQKEKTNDNKIIITRYQTLYYFKKQNYTLLDVELITGRTHQIRAHLASINHPVVGDYKYAKKQYQNNQGNFKHQL--LHSYKIIFDLANYDQDFILKYLDQNQYQTKS 314
>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 = 372, Expect = 6.9e-34, Identities = 93/255 (36%), Positives = 149/255 (58%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQ-IFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +  EE  Q L  +++    +LS S+I + ++ G+I VN KK+  +YK+Q++D +Q I L L+P+K       LEA+ I L+++YEDK++IVVNKP+G++  P       TL N +   LY  +D           + HR+DK T+GL + AKN      L      ++  + YL + +G F ++  T+   I  N  + KQ+  +++     K  +T ++V+EQ +  +L+E QL TG+ HQIRVHMA IGHP+ GD  Y  +
  S:     7 LTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKKSKVSYKVQKDDLIQVIVLPLEPLK-------LEAENIPLDIVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNAL---LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAEEEGTIDAPIGRNPKDRKQMAVVEK----GKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRVHMAYIGHPLAGDPLYGPR 255
>gi|125974463|ref|YP_001038373.1| RluA family pseudouridine synthase [Clostridium thermocellum ATCC 27405] >gi|196252702|ref|ZP_03151354.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM 4150] >gi|125714688|gb|ABN53180.1| pseudouridine synthase, RluA family [Clostridium thermocellum ATCC 27405] >gi|196197869|gb|EDX92714.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM 4150] (320 aa)
Score = 368, Expect = 2.4e-33, Identities = 104/296 (35%), Positives = 174/296 (58%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLY---EKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQK------KDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN---FGFQFPCLTSYKIKFNFDKNH-FLHYLNKLNLEVK 296
           M  I I +++ N+ +   + ++F  L    + K+ +  DIKVN  +   ++ ++ ND + I++  + +    K   L  +   +V YED N+++VNK +G+   PD+ +  +TL + +K+YL    E ++ +    +LCHRLD+ T GL + AKN  TL  +     +  +SKYY CL  GK +KK D LK ++  +E+K  + I D ++K   EIIT Y+V+  K      + ++ LE+ L TG+ HQIR H+A IGHPV+GD KY         G ++  L +YK+KF+F  +   L+YL    ++V+
  S:     1 MRTITITEDKANKRIDKVLRETFPRLPNGALFKAFRKKDIKVNGVRVKEDHIVKLNDRVDIYIIDEILDGVPKAGELNYETAFSVAYEDSNLLIVNKKQGIPVHPDRTQTENTLIDFVKEYLKLKGEFEENSGFTPSLCHRLDRNTGGLVMIAKNSSTLHMVLKKMKSGEISKYYQCLVKGKMEKKEDILKAYLEKDEKKSRVFIKDTKSKNAVEIITGYKVLSYKELPDIGEGISNLEVTLYTGRTHQIRAHLAHIGHPVVGDGKYGINTFNRLLGAKYQALWAYKLKFDFKSDAGILNYLRGKVIQVQ 310
>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 = 363, Expect = 7.9e-33, Identities = 93/255 (36%), Positives = 149/255 (58%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQ-IFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +  EE  Q L  +++    +LS S+I + ++ G+I VN KK+  +YK+Q++D +Q I L L+P+K       LEA+ I L+++YEDK++IVVNKP+G++  P       TL N +   LY  +D           + HR+DK T+GL + AKN      L      ++  + YL + +G F ++  T+   I  N  + KQ+  +++     K  +T ++V+EQ +  +L+E QL TG+ HQIRVHMA IGHP+ GD  Y  +
  S:     7 LTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKKSKVSYKVQKDDLIQVIVLPLEPLK-------LEAENIPLDIVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNAL---LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAEEG-TIDAPIGRNPKDRKQMAVVEK----GKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRVHMAYIGHPLAGDPLYGPR 254
>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 = 353, Expect = 1.2e-31, Identities = 83/264 (31%), Positives = 151/264 (57%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           + I + +E+ ++ L  F+S +  E S +++ + +K+G I+VN K+   NYK+Q  D +++ +       E ++  +EA+P+ L++ YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G  +  + T+   I  ++ ++Q M + +E+   K+ +T + VIE+ +D  ++E +L TG+ HQIRVHM  IG+P+ GD KY  +    F
  S:     4 VNIAVSEEQTSERLDKFLSTTEPEWSRTQVQQWVKDGLIEVNGKQVKANYKVQAGDQIKVEI------PEPEVLDVEAEPMDLDIYYEDADVLVVNKPRGMVVHPAPGHVSGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKYTAVVHGIIQHDTGTIDAPIGRDKKDRQSMTVTKESA--KQAVTHFDVIERFQDFTVVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPRKTVDF 262
>gi|154504965|ref|ZP_02041703.1| hypothetical protein RUMGNA_02475 [Ruminococcus gnavus ATCC 29149] >gi|153794848|gb|EDN77268.1| hypothetical protein RUMGNA_02475 [Ruminococcus gnavus ATCC 29149] (321 aa)
Score = 349, Expect = 3.9e-31, Identities = 85/257 (33%), Positives = 150/257 (58%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQ----PDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           M +I I ++E  Q     + K   +   S + K ++  +I +N KK + N KL + D +++FL  + I+K  +         L+++YED++II++NKP G++ Q     D++     ++  I+ +   ++D      ++C+RLD+ T+G+  A K+   L  L+ +++   + KYYLCL  G  +K S  ++ ++F +E    +EI  +E   +  IIT+YR I+    + LLE+ L+TGK HQIR H+AS+GHP++GD KY
  S:     1 MQEIKITEQEAGQRFDKLLGKYLNKAPKSFLYKMLRKKNITLNGKKASGNEKLAKGDCVKLFLSDETIQKFSETFSGYTNVSLDILYEDEDIILINKPVGMLSQKAARSDESLVEHLISYLIQSHALTEEDLRTFRPSICNRLDRNTSGIVAAGKSMAGLQSLSQMFHDRTIGKYYLCLTAGIIEKPS-RVEGWLFKDERTNKVEILFQERPGSARIITEYRPIKSHDGVTLLEVHLITGKTHQIRAHLASVGHPLIGDHKY 261
>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 = 348, Expect = 4.7e-31, Identities = 84/264 (31%), Positives = 150/264 (56%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           + I + +E+ ++ L  F+S S  E S +++ + +K+G I+VN K+   NYK+Q  D +++ +   P  + L +   EA+ + L++ YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G  +  + T+   I  ++ ++Q M + +E+  +K+ +T + VIE+  D  ++E +L TG+ HQIRVHM  IG+P+ GD KY  +    F
  S:     4 VNIAVSEEQTSERLDKFLSTSEPEWSRTQVQQWVKDGLIEVNGKQVKANYKVQAGDQIKVEI---PEPEALDV---EAEAMDLDIYYEDADVLVVNKPRGMVVHPAPGHVSGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKYTAVVHGIIQHDTGTIDAPIGRDKKDRQSMTVTKES--SKQAVTHFDVIERFDDFTVVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPRKTVDF 262
>gi|167464425|ref|ZP_02329514.1| YlyB [Paenibacillus larvae subsp. larvae BRL-230010] (311 aa)
Score = 346, Expect = 7.1e-31, Identities = 87/252 (34%), Positives = 145/252 (57%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +E   + +  F+S+    +S ++I + IK G I VN K+   NYKL E D +++ +   P  +++ +     +PI L++ YEDK++IVVNKPRG++  P       TL N +   +Y  KD       +   + HR+DK T+GL +AAK+ K    L +     +V++ YL L  G    +  T++  I  + +++++  +  +N  +KE +T + V+E+  D  L E++L TG+ HQIRVHM  IGHP++GD  Y K
  S:    18 EEHAGERIDKFVSECLDGVSRTQIQQWIKEGHISVNEKQVKPNYKLAEGDRIKLNI---PDPEQVDI---RPEPIPLDIYYEDKDVIVVNKPRGMVVHPAPGHSSGTLVNAL---MYHCKDLSGINGEMRPGIVHRIDKDTSGLIMAAKHDKAHASLADQLKEHSVTRKYLALVQGNLAHEQGTVEAPIGRDPKDRKLYTVTEKN--SKEAVTHFVVMERFGDYTLTELKLETGRTHQIRVHMKFIGHPLVGDPAYGK 264
>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 = 341, Expect = 2.7e-30, Identities = 85/260 (32%), Positives = 144/260 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ + +E++N+ +  F++    E S +++ + IK+  + VN K    NYK++END + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVRENDEITVTI---PEPEELDIQPEDMN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>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 = 341, Expect = 2.9e-30, Identities = 85/260 (32%), Positives = 145/260 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ + +E++++ +  F+++   E S S++ + IK+  + VN K    NYK++END + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAEEQKSERIDKFVAEINGEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKENDEITVTI---PDPEELDIQAEDMN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>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 = 340, Expect = 3.6e-30, Identities = 85/260 (32%), Positives = 144/260 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ + +E++N+ +  F++    E S +++ + IK+  + VN K    NYK++END + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKENDEITVTI---PEPEELDIQPEDMN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>gi|168162165|ref|ZP_02597398.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus H3081.97] (302 aa)
Score = 340, Expect = 3.8e-30, Identities = 85/260 (32%), Positives = 144/260 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ + +E++N+ +  F++    E S +++ + IK+  + VN K    NYK++END + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVRENDEITVTI---PEPEELDIQPEDMN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>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 = 337, Expect = 7.6e-30, Identities = 85/260 (32%), Positives = 143/260 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ + +E++N+ +  F++    E S +++ + IK+  + VN K    NYK++END + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V + Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVRENDEITVTI---PEPEELDIQPEDMN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVIRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>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 = 337, Expect = 7.6e-30, Identities = 84/260 (32%), Positives = 144/260 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ + +E++N+ +  F++    E S +++ + IK+  + VN K    NYK++E+D + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREDDEITVTI---PEPEELDIQPEDMN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>gi|167758127|ref|ZP_02430254.1| hypothetical protein CLOSCI_00465 [Clostridium scindens ATCC 35704] >gi|167664024|gb|EDS08154.1| hypothetical protein CLOSCI_00465 [Clostridium scindens ATCC 35704] (333 aa)
Score = 337, Expect = 7.8e-30, Identities = 88/266 (33%), Positives = 147/266 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLR---------LKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE----KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG-NFGFQ 266
           M +I I + E  Q L  F+ K   +   S + K ++  +I +N KK T N KL   DS+++FL          L PIK+E +++       L++I+ED N++ +NKP G++ Q    + +  + + I   L E    +++      ++C+RLD+ T+GL VA K    L  +  L+    + KYYLC   G  +++      + +L + ++  ++      +  I T+Y  I   ++M LL++ L+TG+ HQIR H+AS GHP+LGD KY   G N  FQ
  S:     1 MKEIIISQNEAGQRLDKFLKKYLAKAPGSFLYKMLRKKNIVLNGKKATGNEKLGVGDSVKLFLADDTIGKFAGLAPIKEEYQVSV-----NLDIIHEDANVLFINKPAGMLSQKAAKDDVSMVEHVIAYLLAEGSITQEELRTFRPSICNRLDRNTSGLIVAGKTLIGLQAMARLFKDRTLKKYYLCFVKGGIRRREHI---YGYLAKNEKTNKVTIREAGDTPIETEYVPIAYNQEMTLLKVHLITGRTHQIRAHLASKGHPLLGDYKYGDAGWNRQFQ 272
>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 = 337, Expect = 7.9e-30, Identities = 87/260 (33%), Positives = 141/260 (54%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           I + E N+ L   +S   +E S S++ + IK+GDI VN KK   NY+LQ  D ++I +       E +L  +E + + L++ YED +++VVNKP+G++  P       TL N +   +Y  KD       L   + HR+DK T+GL + AKN     +L    + + V++ Y  L +G    ++ T+   I  +  + +++  +D      K+ +T + V+E+      +E +L TG+ HQIRVHM  IGHP+ GD KY  K    F
  S:     8 ILEHEANERLDKMVSSIREEWSRSQVQQWIKDGDITVNGKKEKANYRLQTGDLVEIEV------PEPELPDIEPEDLHLDIYYEDADVLVVNKPKGMVVHPSNGHFTGTLVNGL---MYHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDYAHEKLAAQLSEKTVTRKYFALVHGNIPHEAGTIDAPIGRDPADRQRMAVVDN----GKDAVTHFHVLERFDRYTFIECRLETGRTHQIRVHMKYIGHPLAGDPKYGPKKTIDF 261
>gi|65321221|ref|ZP_00394180.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus anthracis str. A2012] (302 aa)
Score = 335, Expect = 1.6e-29, Identities = 84/260 (32%), Positives = 143/260 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ + +E++N+ +  F++    E S +++ + IK+  + VN K    NYK++END + + +   P  +EL +   +    L + YED +++VVNKPR ++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVRENDEITVTI---PEPEELDIQPEDMN--LEIYYEDADVLVVNKPRSMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>gi|154685962|ref|YP_001421123.1| YlyB [Bacillus amyloliquefaciens FZB42] >gi|154351813|gb|ABS73892.1| YlyB [Bacillus amyloliquefaciens FZB42] (304 aa)
Score = 334, Expect = 1.8e-29, Identities = 83/276 (30%), Positives = 151/276 (54%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +I ++ E++++ +  F++ + +  S +++ + +K G + VN K    NYK+Q  D + + +   P  +EL +    A+P+ L++ YED++++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ ++Q M + RE+  +K  +T + V+E+ +D  L+E +L TG+ HQIRVHM  IG P+ GD KY  +    F    L +  + F+
  S:     5 EITVQPEQKSERIDKFLASTGENWSRTQVQQWVKEGLVSVNGKSVKANYKMQPGDQVNVTI---PEPEELDV---LAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNGLMAHCNDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGVISHDDGTIDAPIGRDKKDRQSMTVTRES--SKNAVTHFHVLERFQDFTLVECRLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDFNGQALHAGILGFD 275
>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 = 333, Expect = 2.3e-29, Identities = 88/276 (31%), Positives = 149/276 (53%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           I I++ ++ ++Q +  ++S   ++LS S+I+  I+ G I VN +     YK++  D +         + E+ L     K  L++ YED ++IV+NKP+G++  P    +  TL N +   LY  KD       L   + HR+DK TTGL + AKN K    L+     ++V++ Y  L +G  + +  T+   I  + +++Q M +   N  +K   T +RV+E+     L+E +L TG+ HQIRVHM  IGHPV+GD KY+ +         L ++++ F
  S:     4 IDIWVAEDADSQRIDKYLSMVVEDLSRSRIASLIEEGSILVNGEVIRAKYKVKPADHIT-----AAFEDEMALEAAPEKMELDIRYEDHDVIVINKPKGIVVHPANGNQSGTLVNGL---LYHCKDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHASLSKQLQNKSVNRLYYALVHGVIEHEFGTIDAPIGRDPKDRQKMAVIATN--SKPARTHFRVVERFAKYTLVECRLETGRTHQIRVHMQYIGHPVVGDEKYSYRKTMKTNGQLLHAHQLTF 274
>gi|167939375|ref|ZP_02526450.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus AH1134] (284 aa)
Score = 333, Expect = 2.3e-29, Identities = 84/260 (32%), Positives = 142/260 (54%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ +  E++N+ +  F++    E S +++ + IK+  + VN K    NYK++E D + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKEEDEITVTI---PEPEELDIQPEDLN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>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 = 333, Expect = 2.8e-29, Identities = 87/270 (32%), Positives = 146/270 (54%)
  Q:     5 FIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK----KGNFGFQFPCLTSYK 274
           F+  ++E+  L   ++  + +L+ SKI   IK   I VN   TT  YK+ END + + L   P++  +K      K  L++++ED ++IVVNKP+G++  P    +  TL N +  +         L   + HR+DK T+GL + AKN + +  L+     +   + YL + +G FK+++ T+   I  + ++++ M I  +    +  +T ++V+E+  D  L+E +L TG+ HQIRVH+  IGHPV GD  Y      KGN  F    L  +K
  S:     6 FVVSDQESGRLDKVVTNHYPDLTRSKIQNLIKQEQILVNQAPTTNRYKVSENDVIDVTLP-DPVEVSVK----PEKMNLDIVFEDDDVIVVNKPQGMVVHPAPGHENGTLVNGLLDHAPLATVNGELRPGIVHRIDKDTSGLLMVAKNDQAMLSLSAQLKAKTNQRKYLAIVHGNFKEEAGTINAPIGRSKKDRKKMAIVED---GRPAVTHFKVLERFTDYTLIECELETGRTHQIRVHLKYIGHPVAGDPLYGPRNTLKGNGQFLHAKLLGFK 272
>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 = 332, Expect = 3.2e-29, Identities = 81/247 (32%), Positives = 129/247 (52%)
  Q:    11 ENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKY---LYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEE-KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           E Q L  +IS+   E S + + KS+K+G  ++       N ++ EN     F+  K  ++  +   L     L++IYED +I+VVNKP G++  P       TL N +       +   D       + HRLDK T+G+ + AK+ K L +L+  +    V KYY+ LC G  +   DT+   I  +   +Q ME   ++   KE I+ Y+V+       L+++++ TG+ HQIRVHM+ I HPV+GD  Y
  S:    18 ECQRLDRYISQQLPEYSRTFLQKSLKDGAFELVRSGAKINARMSENVIEGDFVHYKMPEEADESTLLPEDIELDIIYEDDDILVVNKPAGMVVHPGAGNYTGTLVNALLGRDLDTFSAMDDGSSRPGIVHRLDKETSGVIIVAKSAKNLDKLSRSFARRDVEKYYVALCRGTIRVGRDTITSHIGRSRSNRQKMENTNDSNRGKEAISHYKVLADNNGATLVKLKIDTGRTHQIRVHMSGINHPVVGDKLY 268
>gi|188589626|ref|YP_001921981.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str. Alaska E43] >gi|188499907|gb|ACD53043.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str. Alaska E43] (322 aa)
Score = 332, Expect = 3.2e-29, Identities = 101/289 (34%), Positives = 164/289 (56%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI-FLRLKPIKKE--LKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEK-----KDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F+ K  K++ LS I K+++  DI+VN KK +  Y L+E D ++I +++  P KKE  +++NF   K      YED+N++VV K  G++  PDK+EK  TL + +  YL EK     +++       C+RLD+ T+GL +  K  + L  +N     + V KYY+ L  GK +    T   +I  N++  I ++ ++E   +K+I  +    +     +LLEI L+TG+ HQIR H+A +G P++GD KY         K  +G ++  L +YK+ F   K    +  NK
  S:     1 MKIEIGANEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGKKQSEKYFLEEGDIVEIKYIKSNPEKKEKFIQVNFSGMK----TAYEDENLLVVEKWPGILVHPDKDEKDPTLTDYVLSYLKEKGSYVPENEITFTPAPCNRLDRNTSGLVMFGKTFEGLKSINETIREDRVRKYYVALVKGKVQDGLHT--GYILKNQDTNISKVYEKEVPDSKKIAMEVTTTQTNGAYSLLEINLITGRSHQIRAHLAHLGSPIIGDDKYGDRKLNSFFKNKYGLEYQYLYAYKLVFKEMKGKVDYLTNK 299
>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 = 332, Expect = 3.4e-29, Identities = 84/260 (32%), Positives = 142/260 (54%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ +  E++N+ +  F++    E S +++ + IK+  + VN K    NYK++E D + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVKEEDEITVTI---PEPEELDIQPEDLN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>gi|168136872|ref|ZP_02580101.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus B4264] (302 aa)
Score = 330, Expect = 5.1e-29, Identities = 84/260 (32%), Positives = 142/260 (54%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ +  E++N+ +  F++    E S +++ + IK+  + VN K    NYK++E D + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAAEQKNERIDKFVTGINNEWSRTQVQQWIKDEVVTVNGKAVKGNYKVKEEDEITVTI---PEPEELDIQPEDLN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTVD-EN--GKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>gi|1373157|gb|AAB57767.1| orf-X; hypothetical protein; Method: conceptual translation supplied by author (303 aa)
Score = 330, Expect = 5.2e-29, Identities = 80/277 (28%), Positives = 143/277 (51%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           I I   +E++++ +  F++ +  + S +++ + +K+G + VN      NYK+Q  D + +      + +   L+ L     L++ YED++++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ ++Q M + R+ K     +T + V+E+ +D  L+E QL TG+ HQIRVHM  IG P+ GD KY  +    F    L +  + F+
  S:     4 IDITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGDQVTV-----TVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLISHDDGTIDAPIGRDKKDRQSMTVTRDGK---NAVTHFHVLERFQDFTLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDFNGQALHAGVLGFD 274
>gi|118726695|ref|ZP_01575316.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum H10] >gi|118663954|gb|EAV70595.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum H10] (303 aa)
Score = 330, Expect = 5.5e-29, Identities = 96/295 (32%), Positives = 157/295 (53%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNK-EIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY-----NKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEV 295
           M  I  ++  E + +   +   F  L+   + K+++  DIKVN  +   +Y +   D + I++    +       F       +V+Y+D N+++VNK  G+   PDKN+K  TL ++++  +Y           LCHRLD+ T+GL + AKN  TL  +        + KYY C+  GK +KK+  L D++  NE+   + I+ E   N  +IIT+YR++     + LLE++L+TG+ HQIR H+A  GHP++GD KY     NK+ N  +Q  C +     F     H L+YLNK  + +
  S:     1 MRSITAEENHEGKKIDRVVRDFFPNLASGMLYKALRKKDIKVNGVRIKEDYIVSFGDKIDIYIIDDYLIGRDDDGF-------SVVYDDDNLLIVNKETGIPVHPDKNQKEATLIDKLQS-IYGPN------LALCHRLDRNTSGLVIIAKNPATLEVMLEKIKNREIQKYYTCIVSGKMEKKNAELVDYLEKNEKLSRVFINPEKTRNSVQIITRYRILASMNSLNLLEVELVTGRTHQIRAHLAYYGHPIIGDGKYGKNAENKQYNAKYQLLCASRLTFNFQSSARH-LNYLNKKTVSI 286
>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 = 330, Expect = 5.6e-29, Identities = 84/260 (32%), Positives = 143/260 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++Q+ + +E++++ +  F+++   E S S++ + IK+  + VN K    NYK++ ND + + +   P  +EL +   +    L V YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G        +   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:     4 VVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVKGNYKVKGNDEITVTI---PEPEELDIQPEDMN--LEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGIIDAPIGRDKKERQSMTVD-EN--GKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>gi|28210692|ref|NP_781636.1| ribosomal large subunit pseudouridine synthase D [Clostridium tetani E88] >gi|28203130|gb|AAO35573.1| ribosomal large subunit pseudouridine synthase D [Clostridium tetani E88] (320 aa)
Score = 330, Expect = 5.7e-29, Identities = 98/276 (35%), Positives = 147/276 (53%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKF 277
           ++I I   E  Q +  F+ K   ++ L  I KSI+ GD+K+N KK    Y L   D ++I       +K      +E    L V YED+N+I+V K  G++   DK     TL + +  YLY+K D     +       C+RLD+ T G+ +  KN ++L +LN +     V KYY  L  GK K      K  I  +E+     I +E K N KEI  + + I+     +LLEIQL+TG+ HQIR H++S+G+P++GD KY  K         +G  +  L +YK+ F
  S:     1 MKIEIGANESGQRMDKFLRKMLTDVPLGAIYKSIRKGDVKINGKKVKEKYSLNLGDIVEIRDIKTNAEKHNDFKAIEGANELKVTYEDQNMIIVEKKPGVLVHSDKKNSDPTLTDYVLSYLYDKGDYVPEEEITFTPASCNRLDRNTAGIIIFGKNYESLKDLNQMIRERHVDKYYQALVCGKIK--DGLYKAHIVKDEKSNKSYIHKEPKKNSKEIEMEVKTIQTCGTYSLLEIQLITGRSHQIRAHLSSLGNPIVGDKKYGSKKLNSFFYNKYGVDYQYLYAYKLIF 287
>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 = 330, Expect = 5.8e-29, Identities = 87/268 (32%), Positives = 142/268 (52%)
  Q:    11 ENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +N+ +  F++    E S +++ + IK+G I VN K    NYK++END + + +   P  +EL +   +    L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ ++Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K         L +  + FN
  S:    14 KNERIDKFVASVNHEWSRTQVQQWIKDGVITVNGKTVKGNYKVKENDEITVTV---PEPEELDIRAEDMN--LEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMYHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYQAIVHGVIPHDKGTIDAPIARDKKDRQSMAVD-EN--GKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLNLNGQALHAGILGFN 275
>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 = 330, Expect = 6.1e-29, Identities = 91/252 (36%), Positives = 138/252 (54%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           EEE   L   I++  K+LS +KI + + + +I VNHK    +YK+Q  DS+ I +   P  K L L   EA+ + L+++YED ++IVVNKP+G++  P       TL N +  + +E  D        + HR+DK T+GL + AKN K    L      +   + YL + +G F+ K+  +   I  N   ++ M +   N   K  +T + V+EQ KD +L++  L TG+ HQIRVHM  IGHP+ GD  Y  K
  S:    10 EEEKGRLDKVIAEKLKDLSRTKIKELVNDKNILVNHKAEKVSYKVQAGDSIDITV---PPAKPLSL---EAQNLNLDIVYEDADVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTHELADSPEGFRPGIVHRIDKDTSGLLMVAKNDKARESLEKQLAEKINKREYLAIVHGNFETKNGVIDAPIGRNPNNRKQMAV---NPKGKAAVTHFTVLEQFKDYSLVKCILETGRTHQIRVHMKYIGHPLAGDPLYGPK 255
>gi|187934776|ref|YP_001887060.1| pseudouridine synthase, RluA family [Clostridium botulinum B str. Eklund 17B] >gi|187722929|gb|ACD24150.1| pseudouridine synthase, RluA family [Clostridium botulinum B str. Eklund 17B] (322 aa)
Score = 329, Expect = 7.3e-29, Identities = 100/289 (34%), Positives = 164/289 (56%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI-FLRLKPIKKE--LKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEK-----KDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F+ K  K++ LS I K+++  DI+VN KK +  Y L+E D ++I +++  P KKE  +++NF   K      YED+N++VV K  G++  PDK+EK  TL + +  YL EK     +++       C+RLD+ T+GL +  K  + L  +N     + V KYY+ L  GK +    T   +I  N++  I ++ ++E   +K+I  +    +     +LLEI L+TG+ HQIR H++ +G P++GD KY         K  +G ++  L +YK+ F   K    +  NK
  S:     1 MKIEIGANEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGKKQSEKYFLEEGDIVEIKYIKSNPEKKEKFIQVNFSGMK----TAYEDENLLVVEKWPGILVHPDKDEKDPTLTDYVLSYLKEKGSYVPENEITFTPAPCNRLDRNTSGLVMFGKTFEGLKSINETIREDRVRKYYVALVKGKVQDGLHT--GYILKNQDTNISKVYEKEVPDSKKIAMEVTTTQTNGAYSLLEINLITGRSHQIRAHLSHLGSPIIGDDKYGDRKLNSFFKNKYGLEYQYLYAYKLVFKEMKGKVEYLTNK 299
>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 = 328, Expect = 1.0e-28, Identities = 85/253 (33%), Positives = 138/253 (54%)
  Q:     5 FIKKE-EENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           FI ++ ++ + L  F+ +   ELS + I + I  G++ VN K    NYKL   D + I L  +P   E+K   +     L+++YED++IIV+NKPRG++  P       TL N + ++       N +    + HRLDK T+G+ + AK  +   +L          + Y+ + +G  K+    +   I  +  +++ M +   N  +KE IT ++V+E+  D  L+E +L TG+ HQIRVHMA IGHPV+GD KY
  S:    11 FIAEDVDKGKRLDLFLVERLPELSRTHIQRIIAAGEVTVNGKAGKANYKLAPADYVTIRLP-EPKPAEIKAEAIS----LDILYEDEDIIVINKPRGMVVHPAAGNYEGTLVNALLRHCDRLSGINGVSRPGIVHRLDKDTSGVMMVAKTDRAHLDLARQIKERTAGRKYVAIVHGNIKENQGIINAPIGRHPTDRKKMAVVFTN--SKEAITTFQVLERFGDYTLVECRLFTGRTHQIRVHMAYIGHPVVGDPKY 259
>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 = 327, Expect = 1.1e-28, Identities = 78/264 (29%), Positives = 137/264 (51%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           I I   +E++++ +  F++ +  + S +++ + +K+G + VN      NYK+Q  D + +      + +   L+ L     L++ YED++++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ ++Q M + R+ K     +T + V+E  +D  L+E QL TG+ HQIRVHM  IG P+ GD KY  +    F
  S:     4 IDITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGDQVTV-----TVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLISHDDGTIDAPIGRDKKDRQSMTVTRDGK---NAVTHFHVLEGFQDFTLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF 261
>gi|153853078|ref|ZP_01994487.1| hypothetical protein DORLON_00472 [Dorea longicatena DSM 13814] >gi|149753864|gb|EDM63795.1| hypothetical protein DORLON_00472 [Dorea longicatena DSM 13814] (340 aa)
Score = 327, Expect = 1.2e-28, Identities = 89/260 (34%), Positives = 148/260 (56%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-----LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE-----KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKE-----IITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           M ++ I   E  Q L   + K   E   S I K ++  +I +N KK T N  L++ DS+++FL    I K         + I     L+VIYED+N+I +NKP G++ Q  K   +  + N +  YL E     +++      ++C+RLD+ T+GL VA K+   L ++  L+    + KYYLC+  G+  + +  ++ ++  +E+   + + +   F+K+     I T+Y  I   ++M LL++ L+TG+ HQIR H+AS GHP+LGD KY  K
  S:     1 MKELIIHDNEAGQRLDKLLRKYLSEAPGSFIYKMLRKKNIVLNGKKATGNEHLKKGDSVKLFLADDTIAKFQAAGKTVEESIKNTVKLDVIYEDQNVIFINKPSGMLSQKAKETDVSVVEN-VTAYLLESGQLTRENLKTFRPSICNRLDRNTSGLIVAGKSLAGLQQMGELFKKRTLKKYYLCIVKGRITEPAH-IRGYLVKDEKTNRVSLSK-GGFSKDAKGLPIETEYVPIAWNEEMTLLKVHLITGRTHQIRAHLASTGHPLLGDYKYGSK 272
>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 = 327, Expect = 1.3e-28, Identities = 82/293 (27%), Positives = 152/293 (51%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN-HFLHYLNKLNLEVKNI 298
           I ++++ + +  F++   +E S +++ + IK+G + +N +    NYK++  D+L++F+    + + +  N     PI  +IYED+++ VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN +    L N    +   + Y  + +G       T+   I  ++ ++Q M +  EN  +++ +T + V+E+  D   +E QL TG+ HQIRVH   IG P+ GD KY  K         L + K+ F   +   F+ +  ++  E+K +
  S:     9 ISEQQQGERIDKFLTAQGEEWSRTQVQQWIKDGHVLINGRTIKSNYKVETGDTLELFVPEPEVLEVVPENI----PI-EIIYEDEDVAVVNKPRGMVVHPAPGHTTGTLVNALMYHCNDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDRAHESLVNQLKAKTTERVYQAIVHGNIPHDHGTIDAPIGRDKVDRQSMTVTEEN--SRDAVTHFTVLERFGDFTFVECQLETGRTHQIRVHFKYIGFPLAGDPKYGPKKTLSIDGQALHAQKLGFEHPRTGEFMRFKVEMPEEMKKL 297
>gi|166031887|ref|ZP_02234716.1| hypothetical protein DORFOR_01588 [Dorea formicigenerans ATCC 27755] >gi|166028340|gb|EDR47097.1| hypothetical protein DORFOR_01588 [Dorea formicigenerans ATCC 27755] (335 aa)
Score = 326, Expect = 1.7e-28, Identities = 92/277 (33%), Positives = 155/277 (55%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKEL-KLNFLEAKPI---LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE----KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRE-NKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY------NKKGNFGFQFPCLTSYKIKF 277
           M +  IK+ E  Q L  ++ K   +   S I K ++  +I +N KK     KL   DS++ FL  + I K        E+ P+   L +IYED NI+++NKP G++ Q  K E +  +   I   L      K++       +C+RLD+ T+G+ VA K+   L  +   +    ++KYYLCL  G  K+ S  ++ ++  +E+   + I R+ ++    I T+Y  +  +K++ LL++ L+TG+ HQIR H+ASIGHP++GD KY      ++   +G +   L SY++ F
  S:     1 MKETIIKENESGQRLDKYLKKYLPQAPGSFIYKMLRKKNITLNGKKAAGQEKLNTGDSIKFFLAEETIDKFTGNAAASESYPVKKDLEIIYEDDNILLINKPAGMLSQKAKKEDVSLVEYVIGYLLSNGSVTKEELLTFHPGICNRLDRNTSGMVVAGKSLAGLQIMGEAFKERTLAKYYLCLVKGCIKETSH-IRGYLKKDEKTNKVMISRKMSEGAAAIETEYEPVAYQKELTLLKVHLITGRTHQIRAHLASIGHPLMGDYKYGNISWNHQYETYGVKTQMLHSYELHF 291
>gi|168182364|ref|ZP_02617028.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf] >gi|182674479|gb|EDT86440.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf] (317 aa)
Score = 324, Expect = 3.1e-28, Identities = 96/276 (34%), Positives = 151/276 (54%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANL----CHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKF 277
           ++I I   E  Q L  F  K  K++ LS I K+I+ G+IKVN +K+     L+E D ++ F       K  K  F+     L + YED+N+++V K  G++   DK E   TL + +  YLY+K D    LE       C+RLD+ T+G+ +  KN + L  LN +     + KYY  L  G+ K      + +I  NE+  + +I  E K N K+I    + I+     + +EI+LLTG+ HQ+R H++ +G+P++GD+KY  K         +G  +  L SYK+ F
  S:     1 MKIVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVESF---NVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGEPTLTDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKIEKYYSSLVKGRIK--DGVYEAYISKNEDTNMSKIYNEPKPNTKKIAMNVKTIQTCGSFSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIF 284
>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 = 323, Expect = 3.4e-28, Identities = 91/274 (33%), Positives = 155/274 (56%)
  Q:     9 EEENQILKDFISKSFKELSLSK------------ISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN 282
           EE+N ILK  +    +E+ L+             I K+ + G IKVN++    +Y L+ +D +++      I +E   + +  K  L+VIYEDK+I+V+NKP+G++  P K  +  TL+N +  Y  EK + + +   L +RLD  T+GL + AKN  +   L+     +   K YL + +G  K+KS  +   I+   E  +  +  E    +  +T+++V+E  +D  L+E+ L TG+ HQIRVH++SIGHP+ GD+ Y K+ +       L +YK++    K+
  S:     2 EEKNNILKIKVQIDEEEIRLNHYLKNHANCSSRFIRKAAREGRIKVNNENVRLSYMLKNDDVIEL-----QINREENQDIVPEKMHLDVIYEDKDIVVINKPKGIVVHPTKRHQNGTLSNGVLYYFKEKNENSIVR--LVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVKSYLAIVHGNLKEKSGVINKPIYRVGEGTLRRVIDER--GQRSVTRFKVVESYEDADLVELTLETGRTHQIRVHLSSIGHPIYGDSLYGKEEHEYIDRQALHAYKLQIPHPKD 278
>gi|187779918|ref|ZP_02996391.1| hypothetical protein CLOSPO_03514 [Clostridium sporogenes ATCC 15579] >gi|187773543|gb|EDU37345.1| hypothetical protein CLOSPO_03514 [Clostridium sporogenes ATCC 15579] (317 aa)
Score = 323, Expect = 3.6e-28, Identities = 96/276 (34%), Positives = 153/276 (55%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANL----CHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKF 277
           ++I I   E  Q L  F  K  K++ LS I K+I+ G+IKVN KK+     L+E D ++ F       K  K  F+     L + YED+N+++V K  G++   DK E   TL + +  YLY+K D    LE       C+RLD+ T+G+ +  KN ++L  LN +     + KYY  L  G+ K      + +I  N++  + +I  E K N K+I  + + I+     + +EI+LLTG+ HQ+R H++ +G+P++GD+KY  K         +G  +  L SYK+ F
  S:     1 MKIVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGKKSKEKNFLEEGDIVESF---NVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGEPTLTDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYESLKTLNEMIRDRKIEKYYSSLVKGRIK--DGIYEAYISKNQDTNMSKIYNEPKPNTKKIAMEVKTIQTCGSFSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIF 284
>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 = 323, Expect = 4.0e-28, Identities = 84/257 (32%), Positives = 137/257 (53%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           M QI    +   + +  F+S++ + LS S I K +K+G I VN      NYK+ END +++F+    +     L+ L     L+++YED +I++VNKP+ ++  P       TL N +   +Y  KD        L   + HR+D  TTG  +  KN K    +       ++++ Y  + +GK K+ +  +   I  +  +++ M    +N   K  +T Y V+ + KD   +E +L TG+ HQIRVHMASIGHP+LGD+ Y
  S:     1 MEQIKFTADRSGERIDRFLSENLENLSRSYIQKLLKDGKISVNQSSVKPNYKISENDKIEVFIPDPEV-----LDILPENIPLDILYEDSDILIVNKPKNMVVHPAPGHYEHTLVNAV---MYHCKDNLSGINGILRPGIVHRIDMDTTGSLLICKNDKAHQIIAEQLKEHSITRRYHAIVHGKIKEDNGVVNAPIGRHPIDRKKMSTKAKN--GKHAVTHYTVLRRFKDYTYIECELETGRTHQIRVHMASIGHPILGDSMY 253
>gi|148379407|ref|YP_001253948.1| pseudouridine synthase, RluA family [Clostridium botulinum A str. ATCC 3502] >gi|153932742|ref|YP_001383785.1| RluA family pseudouridine synthase [Clostridium botulinum A str. ATCC 19397] >gi|153936684|ref|YP_001387335.1| RluA family pseudouridine synthase [Clostridium botulinum A str. Hall] >gi|148288891|emb|CAL82977.1| ribosomal large subunit pseudouridine synthase C [Clostridium botulinum A str. ATCC 3502] >gi|152928786|gb|ABS34286.1| pseudouridine synthase, RluA family [Clostridium botulinum A str. ATCC 19397] >gi|152932598|gb|ABS38097.1| pseudouridine synthase, RluA family [Clostridium botulinum A str. Hall] (317 aa)
Score = 322, Expect = 4.1e-28, Identities = 96/276 (34%), Positives = 151/276 (54%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANL----CHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKF 277
           ++I I   E  Q L  F  K  K++ LS I K+I+ G+IKVN +K+     L+E D ++ F       K  K  F+     L + YED+N+++V K  G++   DK E   TL + +  YLY+K D    LE       C+RLD+ T+G+ +  KN + L  LN +     + KYY  L  G+ K      + +I  NE+  + +I  E K N K+I    + I+     + +EI+LLTG+ HQ+R H++ +G+P++GD+KY  K         +G  +  L SYK+ F
  S:     1 MKIVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVESF---NVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGESTLTDYVLSYLYDKGDYTPELEVTFTPASCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKIEKYYSSLVKGRIK--DGIYEAYISKNEDTNMSKIYNEPKPNTKKIAMNVKTIQTCGSFSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIF 284
>gi|170759830|ref|YP_001786858.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str. Loch Maree] >gi|169406819|gb|ACA55230.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str. Loch Maree] (317 aa)
Score = 322, Expect = 4.2e-28, Identities = 98/289 (33%), Positives = 155/289 (53%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANL----CHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F  K  K++ LS I K+I+ G+IKVN +K+     L+E D ++ F       K  K  F+     L + YED+N+++V K  G++   DK E   TL + +  YLY+K D    LE       C+RLD+ T+G+ +  KN + L  LN +     + KYY  L  G+ K      + +I  NE+  + +I  E K N K+I    + I+     + +EI+LLTG+ HQ+R H++ +G+P++GD+KY  K         +G  +  L SYK+ F     +  +  NK
  S:     1 MKIVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVESF---NVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGEPTLTDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKIEKYYSSLVKGRIK--DGVYEAYISKNEDTNMSKIYNEPKPNTKKIAMNVKTIQTCGSFSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIFRNTMGNLEYMKNK 297
>gi|160942600|ref|ZP_02089845.1| hypothetical protein FAEPRAM212_00074 [Faecalibacterium prausnitzii M21/2] >gi|158446079|gb|EDP23082.1| hypothetical protein FAEPRAM212_00074 [Faecalibacterium prausnitzii M21/2] (316 aa)
Score = 322, Expect = 4.4e-28, Identities = 80/255 (31%), Positives = 144/255 (56%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLN---FLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLY---EKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY-----NKKGNFGFQFPC 269
           L +++++ +  L+  +++K+++   IK+N KK   + ++   D +++F+    +  + ++    +  A+    V+Y+   I++VNKP G+     ++   DTL NR   YL    E K+ +     LCHRLD  T+GL + AK  +      +      V K YLC+ +G+      TL  ++  + ++ I++I  + +   KE+ T+Y  I     +ALL++QL+TG+ HQIR HMASIG P+LGD+KY     N++    +Q  C
  S:    14 LDNYLTQQYPALTPGRLNKALRENKIKLNGKKQPLSTRVMAGDEIKLFILDDVLDADRRVEGPAWKNARTPAQVVYDCPQILIVNKPAGVAVDGPED---DTLLNRALLYLNKQGEYKENDLYTPALCHRLDTGTSGLVIIAKTPEAEELFLSAIKNREVQKTYLCVTFGRPMPPDATLGGYLLKDADRGIVKIVEDKQPGAKEVETRYETIAVSGRLALLKVQLITGRTHQIRAHMASIGCPILGDSKYGNNSANRELKLKYQALC 277
>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 = 322, Expect = 4.4e-28, Identities = 78/255 (30%), Positives = 146/255 (57%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN-----LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           QI I K ++N  +  F+S+     + +K+ ++I  G + VN K T  NYK++  D +++ +   P   E+    +E    L++IYEDK +++VNKP G++  P       TL N +   +Y  +D   ++ N     L HR+DK T+GL V AK ++ +T L + +    + + Y+ L +G+ K+   T++  +  + + +++M++  + +  K  IT ++V+++ + ++L++  L TG+ HQIR HM  IGHP+  D  Y
  S:    21 QISIDKGQKNIRIDKFLSEKLANATRNKVQQAIDAGSVLVNGKPTKANYKIKPMDDIKVMMEKPPRDTEVYPEKIE----LDIIYEDKYLLIVNKPAGMVVHPAHGNWSGTLANAL---VYHFQDLPEMKGNEGRPGLVHRIDKDTSGLLVIAKQEEAMTHLASQFFHHTIDRTYIALVWGEPKEDEGTIEGNVGRSAKNRKVMDVFPDGEQGKHAITHWKVLKRLRYVSLIQCNLETGRTHQIRAHMKYIGHPLFNDAMY 274
>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 = 322, Expect = 4.5e-28, Identities = 87/293 (29%), Positives = 153/293 (52%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN-HFLHYLNKLNLEVKNI 298
           + +E + + +  +++    + S +++ + IK   + VN      NYK+QE D++ + +   P  + L +    A+P+ L++ YED++++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  L +G       T+   I  ++ ++Q M + REN   K  +T + VIE+  D  ++E QL TG+ HQIRVHM  IG P+ GD KY  K    F    L +  + F+  +   ++ +   L  ++KN+
  S:     8 VHEEHKGERIDKYLTAVEADWSRTQVQQWIKEDRVLVNGNAVKANYKVQEGDAVSVQV---PEPEPLDVT---AEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCDDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTALVHGVIPHDHGTIDAPIGRDKKDRQSMTVTREN--GKHAVTHFEVIERFDDFTVVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPKKTVDFNGQVLHAGVLGFDHPRTGEYVEFEAPLPDDMKNL 296
>gi|147678153|ref|YP_001212368.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI] >gi|146274250|dbj|BAF59999.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI] (312 aa)
Score = 322, Expect = 4.9e-28, Identities = 85/261 (32%), Positives = 143/261 (54%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQ 266
           + +E+  + L  F++   + L+ + + K I  G   VN ++   +Y+++  D + +    +P   E+K      +PI L V YED ++IV+NKPRG++  P       TL N +   LY   D       +   + HRLDK T+GL + AKN      L        +++ YL L +G  K++S  +   I  +  +++ M + ++N   K+ +T+YRV+E+ K    +E+ L TG+ HQIRVHM+ IGHPV+GD KY   + +FG +
  S:     9 VGEEDAGKRLDLFLAGEMEGLTRTYVQKLIAEGMASVNGQRGRASYRVKPGDVV-VLQVPEPEGLEIK-----KEPIPLEVYYEDADVIVINKPRGMVVHPADGNYSGTLVNAL---LYHCSDLSGINGVMRPGIVHRLDKDTSGLIMVAKNDTAHLSLARQLKERQITRRYLALVHGLLKEQSGMVDAPIGRDPRDRKKMAVLQKNA--KQAVTRYRVLERFKGYTYIELMLETGRTHQIRVHMSYIGHPVVGDLKYGPSRPHFGLE 265
>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 = 321, Expect = 5.9e-28, Identities = 80/236 (33%), Positives = 129/236 (54%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEA----NLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           E S S++ + IK G + VN      NYKLQ  D +++      + + ++L  L     L +++ED+++IVVNK RG++  P       TL N +   LY   D + +       + HR+DK TTGL + AKN      L +    + + + Y+ L +G+   +  T++  I  +  ++Q M +   N   KE +T +R++E+ KD  L+E +L TG+ HQIRVHM  IGHP+ GD KY  +
  S:    23 EWSRSQVQEWIKTGALLVNGSAVKANYKLQVGDEVEV-----NVPEAVELEVLPEDIPLEIVFEDEDVIVVNKARGMVVHPAAGHTSGTLVNAL---LYHCDDLSGINGVKRPGIVHRIDKDTTGLLMVAKNDLAHESLASQLKDKTIKREYIALVHGELVHELGTIEAPIGRDTNDRQRMTVTDRNA--KEAVTHFRLLERYKDFTLVECKLETGRTHQIRVHMRYIGHPLAGDPKYGPR 253
>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 = 320, Expect = 7.4e-28, Identities = 88/267 (32%), Positives = 143/267 (53%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFP 268
           I   I+ E + + +   I+   +E S S++ + IKNG + VN +    NYK +  DS+ +     P  + L +   E +PI L++ YED++++VVNKPRG++  P       TL N +  +  +    N  L   + HR+DK T+GL + AKN      L      + V++ Y  + +G       T+   I  ++ +++ M +  EN   KE +T +RV+E+ +    +E QL TG+ HQIRVHM  IG+P+ GD +Y  K            G  GF+ P
  S:     4 ITFHIEDEYDGERIDKVIAALNEEWSRSQVQQWIKNGLVTVNGQTVKANYKCEAGDSVAVS---PPEPEPLHV---EPEPIPLDIYYEDEDVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCRDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKAIVHGVIPHDYGTIDAPIGRDKRDRKKMAVTEEN--GKEAVTHFRVLERFRHYTYVECQLETGRTHQIRVHMKYIGYPLAGDPQYGPKKTLAIDGQALHAGVLGFRHP 277
>gi|146296753|ref|YP_001180524.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM 8903] >gi|145410329|gb|ABP67333.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM 8903] (311 aa)
Score = 319, Expect = 9.3e-28, Identities = 95/288 (32%), Positives = 158/288 (54%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY-----NKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLN 289
           I++ I+K      L+  I K +  + +S I K ++ G I+VN +       LQ  D +           +++  +L+ K + ++ +YED NIIV++KP G+   PD N +   +N     ++ +    N L A LCHRLD+ T+GL + AKN++ L E+    +  A+ K YLC+       KS  L  ++  + +K  + I D   +   EI+T+Y++I  K D+ L+++++ TGK HQIR  +A +G  +LGD+KY     NKK N   Q  CL +Y +KF+  +   L YL+
  S:     3 IEMLIEKNFAGMKLEKAIKKKYPTIPMSVIFKLLRKGRIRVNFEVAQKGQILQFGDLISF---------DIEEKYLDQKKVEISKVYEDDNIIVIDKPYGIPSHPDTNNEYSVVN-----WIEDNYSGNQLPA-LCHRLDRNTSGLMIIAKNRQVLNEMLKYMSRRAIKKKYLCITKKVDLPKSGVLVHYLKKDSKKSKVYISDLPAEGYSEIVTRYKIIRGKDDLLLVDVEIETGKTHQIRSQLAHVGLCILGDSKYGDWALNKKYNASIQ--CLCAYYLKFDIGRKGILRYLD 280
>gi|169350066|ref|ZP_02867004.1| hypothetical protein CLOSPI_00806 [Clostridium spiroforme DSM 1552] >gi|169293279|gb|EDS75412.1| hypothetical protein CLOSPI_00806 [Clostridium spiroforme DSM 1552] (322 aa)
Score = 319, Expect = 9.6e-28, Identities = 91/277 (32%), Positives = 148/277 (53%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKK-ELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTE-AVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKF 277
           M +I I + + NQ +  +I K       + I K  +  DIKVN KK    Y L+ ND +++FL     K+     +    K    V+YED ++++V KP GL+   DKNE ++TL N++  YL  K +     +N       HRLD+ T+G+ +  K    L  LN +      + K YL +C GK  +K +     + L+++ Q+  + ++      + T  + ++   D + +E+ L+TG+ HQIRVH++SI HP++GD KY         K  FG     L +YKI+F
  S:     1 MKKIQITENDANQRIDKYIKKLLVNAPTNFIYKMFRKKDIKVNGKKVNEKYILKNNDVVEMFLYEDKFKEFTATKDIYNVKKTFKVLYEDNHVLIVYKPAGLLVHEDKNESVNTLTNQVLSYLANKNELDLSRENTFMPGPVHRLDRNTSGIVIFGKTLGALQVLNEMIKQRHCIEKSYLTICKGKVNQKRNLKGYIVKLDDQAQVKLVSKDYPGALTMETIVKPVKYNNDYSKVEVTLVTGRMHQIRVHLSSIDHPIIGDRKYGDFELNKFVKKEFGLNHQLLHAYKIRF 291
>gi|168217835|ref|ZP_02643460.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC 8239] >gi|182380127|gb|EDT77606.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC 8239] (324 aa)
Score = 319, Expect = 1.2e-27, Identities = 102/289 (35%), Positives = 158/289 (54%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI-FLRLKPIKKELKLNF-LEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN-------LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKF---KKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F+ K  K++ LS I K+++ GDI+VN KK    Y L E D ++I +L+    K++ K NF +     L V+YED+N+++V K  G++   DK     TL + +  YL+ K D  Y+  N        C+RLD+ T+G+    KN + L  LN +     V KYY  L  GK    K ++   KD    +E  +    D E    K+I    +V++     +LLEI+L+TG+ HQ+R H+A +G+P++GD KY         +  FG  +  L +YK+ F      F +  NK
  S:     1 MKIEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLEGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPTLTDYVLSYLFRKGD--YVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKVKKYYCALVKGKIQPGKYEAYISKD----DELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTFKEVPEKFDYLKNK 302
>gi|18310186|ref|NP_562120.1| ribosomal large subunit pseudouridine synthase C [Clostridium perfringens str. 13] >gi|110800940|ref|YP_695859.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC 13124] >gi|169344395|ref|ZP_02865365.1| pseudouridine synthase, RluA family [Clostridium perfringens C str. JGS1495] >gi|182626167|ref|ZP_02953926.1| pseudouridine synthase, RluA family [Clostridium perfringens D str. JGS1721] >gi|18144865|dbj|BAB80910.1| ribosomal large subunit pseudouridine synthase C [Clostridium perfringens str. 13] >gi|110675587|gb|ABG84574.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC 13124] >gi|169297468|gb|EDS79576.1| pseudouridine synthase, RluA family [Clostridium perfringens C str. JGS1495] >gi|177908523|gb|EDT71051.1| pseudouridine synthase, RluA family [Clostridium perfringens D str. JGS1721] (324 aa)
Score = 319, Expect = 1.2e-27, Identities = 102/289 (35%), Positives = 158/289 (54%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI-FLRLKPIKKELKLNF-LEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN-------LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKF---KKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F+ K  K++ LS I K+++ GDI+VN KK    Y L E D ++I +L+    K++ K NF +     L V+YED+N+++V K  G++   DK     TL + +  YL+ K D  Y+  N        C+RLD+ T+G+    KN + L  LN +     V KYY  L  GK    K ++   KD    +E  +    D E    K+I    +V++     +LLEI+L+TG+ HQ+R H+A +G+P++GD KY         +  FG  +  L +YK+ F      F +  NK
  S:     1 MKIEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLEGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPTLTDYVLSYLFRKGD--YVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKVKKYYCALVKGKIQPGKYEAYISKD----DELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTFKEVPEKFDYLKNK 302
>gi|153938225|ref|YP_001390782.1| RluA family pseudouridine synthase [Clostridium botulinum F str. Langeland] >gi|168180094|ref|ZP_02614758.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC 2916] >gi|170754896|ref|YP_001781073.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str. Okra] >gi|152934121|gb|ABS39619.1| pseudouridine synthase, RluA family [Clostridium botulinum F str. Langeland] >gi|169120108|gb|ACA43944.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str. Okra] >gi|182668924|gb|EDT80900.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC 2916] (317 aa)
Score = 318, Expect = 1.2e-27, Identities = 98/289 (33%), Positives = 154/289 (53%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANL----CHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F  K  K++ LS I K+I+ G+IKVN +K+     L+E D ++ F       K  K  F+     L + YED+N+++V K  G++   DK E   TL + +  YLY+K D    LE       C+RLD+ T+G+ +  KN + L  LN +     + KYY  L  G+ K      + +I  NE+  + +I  E K N K+I    + I+     + +EI+LLTG+ HQ+R H+  +G+P++GD+KY  K         +G  +  L SYK+ F     +  +  NK
  S:     1 MKIVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVESF---NVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGEPTLTDYVLSYLYDKGDYTPELEVTFTPASCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKIEKYYSSLVKGRIK--DGVYEAYISKNEDTNMSKIYNEPKPNTKKIAMNVKTIQTCGSFSFIEIELLTGRSHQLRAHLNHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIFRNTMGNLEYMKNK 297
>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 = 317, Expect = 1.6e-27, Identities = 87/240 (36%), Positives = 134/240 (55%)
  Q:    27 SLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN-FGFQ 266
           S S I   I+ G I VN      NYK++  D + + +   P  +ELK+   EA+ I L V+YED++++VVNKP+G++  P       T+ N +   LY  ++       L   + HR+DK T+GL V AKN      L       ++++ YL + +G   + S T+   +  +  +++ M +  +N   KE +T Y V+E+ +D  LLE +L TG+ HQIRVHMA + HPVLGD  Y  + N FG Q
  S:    22 SRSFIQGLIEEGHILVNGAARKANYKVRAMDQITVVI---PPPRELKV---EAENIPLEVLYEDEDVLVVNKPQGMVVHPAPGAWTKTMVNAL---LYHCRNLSGINGVLRPGIVHRIDKDTSGLLVVAKNDLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTVDAPVGRDPADRKKMAVVFQNA--KEAVTHYEVLERFRDFTLLEARLETGRTHQIRVHMAYLKHPVLGDPLYGPRKNPFGLQ 257
>gi|168205450|ref|ZP_02631455.1| pseudouridine synthase, RluA family [Clostridium perfringens E str. JGS1987] >gi|170662972|gb|EDT15655.1| pseudouridine synthase, RluA family [Clostridium perfringens E str. JGS1987] (324 aa)
Score = 317, Expect = 1.7e-27, Identities = 102/289 (35%), Positives = 158/289 (54%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI-FLRLKPIKKELKLNF-LEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN-------LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKF---KKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F+ K  K++ LS I K+++ GDI+VN KK    Y L E D ++I +L+    K++ K NF +     L V+YED+N+++V K  G++   DK     TL + +  YL+ K D  Y+  N        C+RLD+ T+G+    KN + L  LN +     V KYY  L  GK    K ++   KD    +E  +    D E    K+I    +V++     +LLEI+L+TG+ HQ+R H+A +G+P++GD KY         +  FG  +  L +YK+ F      F +  NK
  S:     1 MKIEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLEGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAATLTDYVLSYLFRKGD--YVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKVKKYYCALVKGKIQPGKYEAYISKD----DELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTFKEVPEKFDYLKNK 302
>gi|110803565|ref|YP_698546.1| pseudouridylate synthase [Clostridium perfringens SM101] >gi|110684066|gb|ABG87436.1| pseudouridylate synthase [Clostridium perfringens SM101] (324 aa)
Score = 317, Expect = 1.8e-27, Identities = 101/289 (34%), Positives = 159/289 (55%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI-FLRLKPIKKELKLNF-LEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN-------LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKF---KKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F+ K  K++ LS I K+++ GDI+VN KK    Y L + D ++I +L+    K++ K NF +     L V+YED+N+++V K  G++   DK     TL + +  YL+ K D  Y+  N        C+RLD+ T+G+    KN + L  LN +     V+KYY  L  GK    K ++   KD    +E  +    D E    K+I    +V++     +LLEI+L+TG+ HQ+R H+A +G+P++GD KY         +  FG  +  L +YK+ F      F +  NK
  S:     1 MKIEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLDGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPTLTDYVLSYLFRKGD--YVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKVNKYYCALVKGKIQPGKYEAYISKD----DELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTFKEVPEKFDYLKNK 302
>gi|168209672|ref|ZP_02635297.1| pseudouridine synthase, RluA family [Clostridium perfringens B str. ATCC 3626] >gi|168213116|ref|ZP_02638741.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE str. F4969] >gi|170712270|gb|EDT24452.1| pseudouridine synthase, RluA family [Clostridium perfringens B str. ATCC 3626] >gi|170715381|gb|EDT27563.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE str. F4969] (324 aa)
Score = 316, Expect = 2.2e-27, Identities = 101/289 (34%), Positives = 158/289 (54%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI-FLRLKPIKKELKLNF-LEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN-------LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKF---KKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F+ K  K++ LS I K+++ GDI+VN KK    Y L + D ++I +L+    K++ K NF +     L V+YED+N+++V K  G++   DK     TL + +  YL+ K D  Y+  N        C+RLD+ T+G+    KN + L  LN +     V KYY  L  GK    K ++   KD    +E  +    D E    K+I    +V++     +LLEI+L+TG+ HQ+R H+A +G+P++GD KY         +  FG  +  L +YK+ F      F +  NK
  S:     1 MKIEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLDGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPTLTDYVLSYLFRKGD--YVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKVKKYYCALVKGKIQPGKYEAYISKD----DELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTFKEVPEKFDYLKNK 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 = 316, Expect = 2.4e-27, Identities = 88/267 (32%), Positives = 143/267 (53%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFP 268
           I   I++E + + +   I+    E S S++ + IKNG + VN +    NYK +  D++ I     P  + L +   E +PI L++ YED++++VVNKPRG++  P       TL N +  +  +    N  L   + HR+DK T+GL + AKN      L      + V++ Y  + +G       T+   I  ++ +++ M +  EN   KE +T +RV+E+ +    +E QL TG+ HQIRVHM  IG+P+ GD +Y  K            G  GF+ P
  S:     4 ITFHIEEEYDGERIDKVIAALNDEWSRSQVQQWIKNGLVTVNGRTVKANYKSELGDTVAIS---PPEPEPLHV---EPEPIPLDIYYEDEDVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCRDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKAIVHGVIPHDYGTIDAPIGRDKRDRKKMAVTDEN--GKEAVTHFRVLERFRQYTYVECQLETGRTHQIRVHMKYIGYPLAGDPQYGPKKTLSIEGQALHAGVLGFRHP 277
>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 = 315, Expect = 2.9e-27, Identities = 82/253 (32%), Positives = 137/253 (54%)
  Q:     5 FIKKEEE--NQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKL-NFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           F   EE   N+ +  F+S    + S S I K IK+G ++VN K+   NYKL   D +++ +       EL++ + L  +  L+++YED +++VVNKP+G++  P       TL N +  +  E        +   + HR+D  TTG  +  KN +    L       ++++ Y  + +G  K+ S T+   I  +  +++ M +   +   +E +T YRV+E+  +   +E +L TG+ HQIRVHMASIGHP+LGD  Y
  S:     6 FFTAEETVTNERIDKFLSAQMPDRSRSYIQKLIKDGLVEVNGKQVKTNYKLGSEDEVKLQI------PELEVPDILPEEIPLDILYEDTDLLVVNKPKGMVVHPAPGHYTGTLVNALMYHCRENLSGINGVMRPGIVHRIDMDTTGSLLVCKNDRAHQILAEQLKDHSITRRYEAIVHGNLKEDSGTVNAPIGRHPTDRKKMSVHAPH--GREAVTHYRVLERFGNYTHIECELETGRTHQIRVHMASIGHPILGDLVY 256
>gi|110597884|ref|ZP_01386166.1| Pseudouridine synthase, RluD [Chlorobium ferrooxidans DSM 13031] >gi|110340461|gb|EAT58947.1| Pseudouridine synthase, RluD [Chlorobium ferrooxidans DSM 13031] (349 aa)
Score = 315, Expect = 3.1e-27, Identities = 81/243 (33%), Positives = 132/243 (54%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL---YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEE--KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +  ++++  +  + +K+ ++I+ G + VN K+   NY+++  D++QI   L+P   EL     E  PI ++IYED++++V+NK  G++  P       TL N I  ++    E+ DK+ L   + HRLDK T+GL + AKN   L  L   +    V K Y  + +G   ++S T+   I  +++  K +     E K  K  IT Y V E     +LL + L TG+ HQIR HM  +GH +LGD  Y
  S:    36 IDQYLTRQVENATRNKVQEAIEEGRVLVNEKRVKSNYRIKSCDTIQITF-LRPPAPELAP---EDIPI-DIIYEDEDLMVINKKPGMVVHPAFGNWTGTLANAILHHIGIGAEELDKSSLRPGIVHRLDKNTSGLIIVAKNPVALHRLARQFADRQVVKIYKAIVWGVPAEQSGTITTNIGRSKKDRKVMANFPYEGKDGKTAITDYSVTENLHWFSLLSLTLHTGRTHQIRAHMQHLGHQILGDETY 278
>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 = 314, Expect = 4.3e-27, Identities = 84/260 (32%), Positives = 135/260 (51%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           M + F  + ++ + +  ++S+   + S S I K IK   + VN K    NY+L   D ++I L   P  KE  +   E  P L+++YEDK+II+VNKP+ ++  P       TL N +  +           +   + HR+D  TTG  VA KN      L+      ++ + Y+ + +G  K++  T+   I  +  E++ M I   N   +E +T Y+V+E+  D   +  +L TG+ HQIRVHMAS+GHP+LGD  Y  K
  S:     1 MKEFFTVENQDGERIDRYLSEELADRSRSYIQKLIKENYVTVNQKPVKANYRLSLGDRVEIDL---PEAKEPDIR-PEDIP-LDILYEDKDIIIVNKPKQMVVHPAPGHYSQTLVNALMYHCGSDLSGINGTMRPGIVHRIDMDTTGSLVACKNDMAHQSLSRQLKEHSIRRIYVAIVHGNIKEEYGTVNAPIGRHPTERKKMSIHSRN--GREAVTHYQVLERFGDYTYIRCELETGRTHQIRVHMASLGHPLLGDGVYGPK 256
>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 = 313, Expect = 4.8e-27, Identities = 82/260 (31%), Positives = 135/260 (51%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +IQ  I  E +N+ +   I+   +E S SK+ + IK+G + VN +    NYK    D + + L      +   L+ +     L++ YED +++VVNKPRG++  P       TL N +  +  +    N  L   + HR+DK T+GL + AKN      L +    + V++ Y  + +G       T+   I  ++ +++ M +  EN   KE +T +RV+E+ +    +E QL TG+ HQIRVHM  IG+P+ GD +Y  K
  S:     3 VIQFHIDAEYDNERIDKVIAALNEEWSRSKVQQWIKDGLVTVNDQHVKANYKSSAGDVVVVRL-----PEPEPLHVVPENIPLDIYYEDADVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCTDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHQSLVDQLVKKTVTRKYKAIVHGVIPHDYGTIDAPIGRDKRDRKKMTVTEEN--GKEAVTHFRVLERFRHYTFVECQLETGRTHQIRVHMKYIGYPLAGDPQYGPK 257
>gi|167768022|ref|ZP_02440075.1| hypothetical protein CLOSS21_02565 [Clostridium sp. SS2/1] >gi|167710351|gb|EDS20930.1| hypothetical protein CLOSS21_02565 [Clostridium sp. SS2/1] (323 aa)
Score = 313, Expect = 4.9e-27, Identities = 88/260 (33%), Positives = 150/260 (57%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKK-ELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKY-----LYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           M ++ I   EE Q L   +SK   +   S + K ++  +IK+N KK T N KL + D + I+L    I K   ++   + K  L+V+YED+N+I+VNKP G++ Q  K E I ++N++I  Y     L  +K+   ++ ++C+RLD+ TTG+ +   + + L  +  +     + KYYLC+  GK +  S  +  ++  +E+   +++ ++       I T Y  +    +  LL+++L+TGK HQIR H+ASIGHP++GD KY  K
  S:     1 MRELNITTREEGQRLDKILSKYLNKAPKSFVYKMLRKKNIKLNGKKATGNEKLSQGDQVCIYLAEDTINKFREEVKAGKQKIKLDVLYEDENVIMVNKPWGILSQKSKPEDI-SINDQIIPYAVNQGLISEKELQVVKPSICNRLDRNTTGIIICGISIEGLQTMAEMLKHRDMEKYYLCIVKGKIEG-SQKVSAYLKKDEKTNKVKVSKQEIAGASHIETAYEPVISNDEFTLLKVELITGKTHQIRAHLASIGHPLIGDFKYGDK 265
>gi|167747168|ref|ZP_02419295.1| hypothetical protein ANACAC_01882 [Anaerostipes caccae DSM 14662] >gi|167654128|gb|EDR98257.1| hypothetical protein ANACAC_01882 [Anaerostipes caccae DSM 14662] (329 aa)
Score = 313, Expect = 5.1e-27, Identities = 81/261 (31%), Positives = 139/261 (53%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFL---RLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE-----KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           M +I I   EE Q L   ++K   +   S + K ++  +IK+N KK + + KL+  D + +++    +   ++E +    +A   L+VIY+D N++++NKP G++ Q  K   I ++N  I  Y  E     + D   +  ++C+RLD+ TTGL +A  + + L  +  +    +V KYY C+  G   KK+         + E ++   +R+      I T Y  +       LL ++L+TGK HQIR H+A +G P+ GDTKY  +G
  S:     1 MKEIRISDREEEQRLDKLLAKYLNKAPKSFLYKMLRKKNIKLNGKKASGSEKLKSGDVVCVYMADATIASFREEPRAERRKAD--LSVIYQDSNVLIINKPYGMLSQKAKPSDI-SVNELIVPYCLEHGILKESDLELVRPSVCNRLDRNTTGLLIAGISLEGLQTMAEVLRDRSVRKYYYCIVKGMVNKKTRISGYICKDHRENKVSFSERKISGGSRIETAYEPMAAGHGFTLLRVELITGKTHQIRAHLAGMGFPLAGDTKYGDRG 266
>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 = 313, Expect = 5.5e-27, Identities = 80/273 (29%), Positives = 140/273 (51%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           I+++++ + +   +S    E S ++I   I +G+IKVN       YK++  D + I      + +   L+ +     L+++YED +++VVNKP+G++  P       TL N +   +Y+ KD       +   + HR+DK T+GL + AKN      L +    + V++ Y+ L +G       T+   I  +++ +  +   +N   K  +T + V+E+  D  L+E +L TG+ HQIRVHM  IG P++GD KY  K    F    L +  + FN
  S:     8 IEEQQQGERIDKALSSLQSEWSRTQIGNWISDGNIKVNGDAVKAKYKVKAGDVIAI-----DVPEAEPLDVIAENLALDIVYEDADVLVVNKPKGMVVHPAPGHMTGTLVNGL---MYQCKDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNKTVTRKYIALVHGHIAHDKGTIDAPIGRDQKDRQKQAIVDN--GKHAVTHFHVVERFGDYTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPKKTIDFGGQVLHAATLGFN 274
>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 = 313, Expect = 5.7e-27, Identities = 82/236 (34%), Positives = 131/236 (55%)
  Q:    24 KELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRL-KPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +++S S++   I +G + VN      NYK+ + D  +I L++ +P   E+     E  P L + +ED ++IVVNKPRG++  P       TL N +   ++  KD       L   + HR+DK TTGL +AAKN K    L       +V++ YL L +G       T+   I  + +++++  +   N  +K  +T + V+E+  D +LLE++L TG+ HQIRVHM  IGHP++GD  Y K
  S:    47 EDVSRSQVQLWIADGHVSVNDGPIKSNYKVSQGD--RIVLKVPEPSAVEI---IPEDIP-LEIAFEDGDVIVVNKPRGMVVHPAPGHSSGTLVNAL---MFHCKDLSGINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEHSVNRRYLALVHGNISHDQGTIDAPIGRDAQDRKLYTVTDRN--SKHAVTHFTVVERFGDYSLLELKLETGRTHQIRVHMKYIGHPLVGDPVYGK 277
>gi|167756776|ref|ZP_02428903.1| hypothetical protein CLORAM_02325 [Clostridium ramosum DSM 1402] >gi|167702951|gb|EDS17530.1| hypothetical protein CLORAM_02325 [Clostridium ramosum DSM 1402] (328 aa)
Score = 312, Expect = 7.2e-27, Identities = 91/277 (32%), Positives = 147/277 (53%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKL-NFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTE-AVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKF 277
           M ++ I + + NQ +  ++ K       + I K  +  DIKVN KK    Y L  +D +++FL     K+  +  +  E     +V+YEDK++++V KP GL+   D NE I+TL N++  YL  K +     +N       HRLD+ T+G+ +  K    L  LN +      + K YL +C G+   + +     I L  + Q+  + ++      + T  R ++   D +L+E+ L+TG+ HQIRVH++SI HP++GD KY         K  FG     L +YKIKF
  S:     7 MKKLKITENDANQRIDKYLKKLLVNAPNNFIYKMFRKKDIKVNGKKVDEKYILSLDDEVEMFLYDDKFKEFTETKSIYEVNKTFSVLYEDKHVLIVFKPAGLLVHEDANESINTLTNQVLSYLASKNELDLSRENTFMPGPVHRLDRNTSGIVIFGKTLAALQNLNEMIKQRHCIEKKYLTICRGQLNHQRNLHGYMIKLENQAQVKLVKKDYPGALTMETIVRPLKYNCDYSLVEVTLITGRMHQIRVHLSSIEHPIIGDRKYGDFELNKYIKKTFGLNNQLLHAYKIKF 297
>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 = 312, Expect = 7.7e-27, Identities = 79/267 (29%), Positives = 139/267 (52%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHF 284
           F+    +  + +KI ++ ++G+I+ N +    NY+++  D++++     P +     N L  + I L+++YED+ ++VVNKP G++  P       TL N +  +L +    +     L HR+DK T+GL V AK +  +  L   +  +   + YL L +G     S T++  I  N + ++ M++  +    KE +T YRV E+   + L+  +L TG+ HQIRVHM  IGH +  D++Y   G+   +    T YK    F +N F
  S:    35 FLMTRIRNATRNKIQQAARDGNIRANEQVIKQNYRVKPGDTIRVLFEHPPYE-----NLLLPEDIPLDIVYEDEVLLVVNKPAGMVVHPGHGNYTGTLVNALVHHLDQLPLNSDNRPGLVHRIDKETSGLLVIAKTEAAMANLARQFFDKTTRREYLALVWGNVADDSGTVEGPIGRNPKNRLQMQVFPDGSQGKEAVTHYRVEERLGYVTLVSCRLETGRTHQIRVHMQHIGHTIFNDSRYG--GDRILKGTSFTKYK---QFVENAF 293
>gi|168139860|ref|ZP_02583089.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus G9842] (302 aa)
Score = 311, Expect = 9.2e-27, Identities = 82/250 (32%), Positives = 131/250 (52%)
  Q:    11 ENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +N+ +  F++    E S S++ + IK+  + VN K    NYK++E D + +      I     L+       L + YED +++VVNKPRG++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   I  ++ E+Q M +D EN   K  +T ++V+E+ KD  L+E +L TG+ HQIRVHM  IG+P+ GD KY  K
  S:    14 KNERIDKFVAGINNEWSRSQVQQWIKDDVVTVNGKAVKVNYKVKEEDEITV-----TIPDPEALDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIGRDKKERQSMTVD-EN--GKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPK 257
>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 = 311, Expect = 9.5e-27, Identities = 86/240 (35%), Positives = 134/240 (55%)
  Q:    27 SLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN-FGFQ 266
           S S I   I+ G + VN      NYK++  D + + +   P  +ELK+   EA+ I L ++YED++++VVNK +G++  P       TL N +   LY  ++       L   + HR+DK T+GL V AKN      L       ++++ YL + +G   + S T++  I  +  +++ M +  +N   KE +T Y V+E+ +D  LLE +L TG+ HQIRVHMA + HPVLGD  Y  + N FG Q
  S:    56 SRSFIQGLIEEGHVLVNGAARKANYKVRAMDQIAVVI---PPPRELKV---EAENIPLEILYEDEDVLVVNKSQGMVVHPAPGAWTKTLVNAL---LYHCRNLSGINGVLRPGIVHRIDKDTSGLLVVAKNDLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTVEAPIGRDPADRKKMAVVFQNA--KEAVTHYEVLERFRDFTLLEARLETGRTHQIRVHMAYLKHPVLGDPLYGPRKNPFGLQ 291
>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 = 310, Expect = 1.2e-26, Identities = 88/279 (31%), Positives = 142/279 (50%)
  Q:     9 EEENQILKDFISKSFKELSLSK--ISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFL--NEEKQIMEIDRENKFNKEIITKYRVIEQ-KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN-HFLHY 287
           E+  + +  F++ S  E S+S+  + + IK+G + VN      NYKL   D + I +   P  ++  +   E  P L+++YED ++IV+NKPRG++  P       T+ N +   +Y  KD       L   + HR+DK T+GL +AAKN      L       +VS+ Y+ L +G       T+   I    N+ K     DR +K     +T + V+E+   D  ++E+QL TG+ HQIRVHM  IG+P+ GD  Y +      +   L +  + F   +   FL +
  S:    20 EQAGERIDKFVTDSLNEDSISRTQVQEWIKSGAVLVNQNTVKPNYKLSSGDHVGIRV---PEPEDAAI-VAEDIP-LDIVYEDADVIVINKPRGMVVHPAPGHSSGTVVNAL---MYHCKDLSGINGVLRPGIVHRIDKDTSGLLMAAKNDLAHVSLAEQLKDHSVSRKYIALVHGNLPHDQGTIDAPIGRDQNDRKLFTVTDRNSK---HAVTHFAVLERIADDYTIVELQLETGRTHQIRVHMKYIGYPLAGDPMYGRNKTVALKGQALHAAVLGFKHPRTGEFLEF 297
>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 = 309, Expect = 1.4e-26, Identities = 79/243 (32%), Positives = 136/243 (55%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL-----YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           L  F++   +  S ++I  +   G+I VN K    +YK++  D  +I L +   K+E+++   E  P L + YED ++++VNKP G++  P       TL N +  YL     +++ D   + A L HR+DK T+GL V AKN++    L   +    +++ Y+ L +G F++   T+   I  + +++Q M +  +    K  +T YRV+++   + L+E +L TG+ HQIRVHM   GHP+ GD +Y
  S:    41 LDKFLTIHMERCSRNRIQTAADAGNILVNGKPAKSSYKVKPGD--RISLVMPYPKREIEI-IPENIP-LEIPYEDDDLLLVNKPAGMVVHPGHGNYSATLVNALTYYLQNLPLFQEGD---MRAGLVHRIDKNTSGLLVIAKNERAHARLAKQFFDHTITRRYVALVWGNFEEDEGTITGNIGRSPKDRQKMWVFEDGSDGKHAVTHYRVLKRYGYVTLIECRLETGRTHQIRVHMQWKGHPLFGDERY 282
>gi|126649705|ref|ZP_01721941.1| YlyB [Bacillus sp. B14905] >gi|126593424|gb|EAZ87369.1| YlyB [Bacillus sp. B14905] (303 aa)
Score = 308, Expect = 1.7e-26, Identities = 79/273 (28%), Positives = 140/273 (51%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           I+++++ + +   +S    E S ++I   + +G+IKVN       YK++  D + I      + +   L+ +     L+++YED +++VVNKP+G++  P       TL N +   +Y+ KD       +   + HR+DK T+GL + AKN      L +    + V++ Y+ L +G       T+   I  +++ +  +   +N   K  +T + V+E+  D  L+E +L TG+ HQIRVHM  IG P++GD KY  K    F    L +  + FN
  S:     8 IEEQQQGERIDKALSSLQSEWSRTQIGNWVSDGNIKVNGDAVKPKYKVKAGDVIAI-----DVPEAEPLDVIAENLALDIVYEDADVLVVNKPKGMVVHPAPGHLTGTLVNGL---MYQCKDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNKTVTRKYIALVHGHIAHDKGTIDAPIGRDQKDRQKQAIVDN--GKHAVTHFHVVERFGDYTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPKKTIDFGGQVLHAATLGFN 274
>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 = 308, Expect = 1.8e-26, Identities = 93/277 (33%), Positives = 148/277 (53%)
  Q:     1 MIQIFIKKEEENQILKD-FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           M  +FI  EE   I  D ++S+   ++S S I K +K+ +I +N K    NYK+Q +D + I      I K ++ N +     L++IYED + ++VNKP+ ++  P       TL N +   +Y  K+        L   + HR+DK TTG  +  KN  +   +       ++++ Y+ +  G  K +S T+   I  +   ++ M I+ +N   KE +T Y+V+++      +E QL TG+ HQIRVHMASI HP+LGDT YN  K  F  +  CL +  I F
  S:     1 MNNLFIVDEELFDIRIDRYLSELLPDVSRSFIQKLLKDNEILLNDKPVKANYKVQPSDKINI-----NIPKPVEANIVAENIPLDIIYEDDDFLIVNKPKDMVVHPAPGHYTGTLVNGL---MYHCKNHLSNINGVLRPGIVHRIDKDTTGALIICKNDYSHNFIAEQLKVHSITRKYVGIVQGVVKDESGTINAPIGRHPVNRKEMAINHKN--GKEAVTHYKVLKRFDKYTFMEFQLETGRTHQIRVHMASIHHPLLGDTVYNHNKCPFKLEGQCLHAKTIGF 275
>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 = 308, Expect = 1.8e-26, Identities = 82/243 (33%), Positives = 137/243 (56%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           L  F++   +++S S I K I++G + V+ K    N+KL+  +++ + +   P  +ELK+   E + I L++ YED ++IVVNKPRG++  P +     TL N +  + ++    N  +   + HRLDK T+GL +AAK+ +    L        V++ Y  L +   K    T+   I  +  ++Q M +   N  +K  +T ++V+E+  D  L+E +L TG+ HQIRVHMA IG P++GD KY
  S:    17 LDVFLANQCQDISRSYIQKLIEDGLVTVDGKPARANHKLRVEETIHMQI---PPAEELKV---EPENIPLDIYYEDSHVIVVNKPRGMVVHPAEGNIAGTLVNALLYHCHDLSGINGIMRPGIVHRLDKDTSGLIMAAKHDQAHQSLARQLKDRTVTRRYQALVHHNIKGDFGTINAPIGRDPRDRQKMAVVERN--SKNAVTHFQVLERFGDYTLIECRLETGRTHQIRVHMAYIGFPLVGDPKY 254
>gi|160943193|ref|ZP_02090429.1| hypothetical protein FAEPRAM212_00679 [Faecalibacterium prausnitzii M21/2] >gi|158445432|gb|EDP22435.1| hypothetical protein FAEPRAM212_00679 [Faecalibacterium prausnitzii M21/2] (329 aa)
Score = 308, Expect = 1.9e-26, Identities = 95/297 (31%), Positives = 161/297 (54%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLR--------LKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL-----YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI---DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY-NKKGN--FGFQFPCLTSYKIKF-NFDKNHFLHYLNKLNLEVKN 297
           M Q      ++   L  F+    ++   S + KS +N  +KVN KK    Y+LQ  D +++++          KP++K         +P + VIYED+N+ V+ KP  L+C  D+    + L +   +YL     Y+   +N  +  +C+RLD+ T GL +AAKN   L ++N +  T+ + K Y  +  G    +S     +   +E+   + I     +++  K+IIT   V+      AL +I L+TG+ HQIR H+A +G PVLGD KY N+K N   G +   L + +I F +  + + LHYL+   +++K+
  S:     1 MKQFTATANDDGVRLSRFVQSVTRDFPTSLLYKSFRNKRVKVNGKKAAPEYRLQAGDLIELYINDEFFPPEGAKPVQKAAPKK-QPNQPKVTVIYEDENLAVLYKPTHLLCHSDRTGDAN-LVDAFTQYLTQKGEYDPHGENRFKPGICNRLDRGTEGLVIAAKNYAALRDMNEIIRTDLLKKEYYTITVGI--PQSGRFTAWWEHDEKNNKVSIHAHQSQDERRKQIITDVDVLRTAGPFALCKIGLVTGRTHQIRAHLAYLGKPVLGDIKYGNRKMNERTGTKTQALCAVRISFLDVPEENTLHYLSGKVIKLKD 313
>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 = 308, Expect = 2.0e-26, Identities = 81/259 (31%), Positives = 133/259 (51%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL---YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSY 273
           +  ++++  +  + +K+ ++I++G + VN K    NY+++  DS+++   L+P   EL     E  PI +++YED +++VVNK  G++  P       TL N I  +     E+ + + L   + HRLDK T+GL + A+N   L  L   +    VSK Y  + +G  + +  T+   I  +  + K +     E    K  IT YRV E     +L E+ L TG+ HQIR HM  +GH +LGDT Y         FP   S+
  S:    40 IDQYLTRQVENATRNKVQEAIEDGRVLVNGKSVKSNYRVKSCDSIEMTF-LRPPAPELAP---EDIPI-DIVYEDSDLMVVNKAPGMVVHPAFGNWTGTLANAILHHFGTDAEELETDELRPGIVHRLDKDTSGLIIVARNPTALHRLARQFADRKVSKLYTAILWGVPEPQEGTIHTNIGRSRRDRKVMANFPYEGLEGKTAITDYRVTENLHWFSLAELTLHTGRTHQIRAHMQHLGHQILGDTTYGGASLRTLDFPRSESF 298
>gi|110004533|emb|CAK98870.1| hypothetical rna pseudouridylate synthase c protein [Spiroplasma citri] (312 aa)
Score = 307, Expect = 2.3e-26, Identities = 101/290 (34%), Positives = 159/290 (54%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHK-KTTWNYKLQENDSLQIF---LRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNR--IKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTEL-NNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEII-TKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++ + +K  + NQ + +FI K F+   LS I K  +N  IKVN+K     NYKLQ  D + IF   L +    + +  N +E  P L V+YED NI+VV+KP G+      +  +D +     I+K+ Y  +D+     +  HRLDK T GL + AKN+ TL  L   +   E++ K YL  C G  K+   TL  +++ NE+KQ M   +  + + +++ T +RV  Q  +   LE+ L+TG+KHQIR  ++ + HP++ D KY  K         L +  + F+   +H L YLN+
  S:     6 VVTLTVKANDVNQTIFNFIKKMFQTTPLSVIYKLFRNKKIKVNNKVMKERNYKLQLGDQIIIFDKNLVVTERNQAVTYNNVETLP-LQVVYEDDNILVVDKPHGVEMYSKFHTSLDAMVQHYLIQKHEYHPEDEQSFVISHVHRLDKLTRGLVLYAKNKITLDLLLAKINQKESIEKKYLAKCEGIIKETDFTLTGYLYKNEDKQKMVFTKTVQPHAKVVKTHFRVQHQLTNATWLEVTLITGRKHQIRASLSYLHHPIVNDIKYGAKQETKEYMIVLYATTLIFHQLPDH-LSYLNE 301
>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 = 307, Expect = 2.6e-26, Identities = 86/274 (31%), Positives = 151/274 (55%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-KGNFGFQFPCLTSYKIKF 277
           + + +E E + L  F+++   ELS S +   I+NG+I+V+ K+   +Y+L+  + + + +   P  +ELKL   +A+ I L+ IY+DK+I V++KP+G++  P      +TL N +  +L +    N  L   + HRLDK T+G+ V AKN     +L       ++++ Y+ L +G  K+   +++  I     KQ  +        +  ++ Y+V+E+  +  LL+++LLTG+ HQIRVH A I HPV+GD  Y   K   G     L ++ + F
  S:     7 LLVDEEMEGERLDAFVTEQLDELSRSLVKTLIENGEIRVDSKQQKPSYRLKAGEEIIVEI---PAVRELKL---KAQDIPLSFIYQDKDIAVIDKPKGMVAHPAHGNWENTLVNALLFHLKDLSGINGELRPGIVHRLDKDTSGVMVIAKNDMAHRQLAAQIKDHSINREYITLVHGIIKENLGSIEAPI--GRSKQDRKKMAVIAGGRPAVSNYQVLERLGNYTLLKVKLLTGRTHQIRVHFAYIKHPVVGDPLYGSGKKQLGLDTQALHAHLLGF 275
>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 = 307, Expect = 2.8e-26, Identities = 84/275 (30%), Positives = 148/275 (53%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQ-KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           Q  + ++E    L   ++  F E + S + K  K+  + V+  +   NYK++E +  ++ L+   + K  +L+    K  L+++YED++II++NKP+ ++  P       TL N + ++  ++       L   + HR+DK TTG+ +  KN      L        +++ Y  +     K++S T+   I  + ++++ M IDRE    +  +T YRV+E+ K+    +E +L TG+ HQIRVHMASIGHP+LGDT Y  KK  +  +  CL +  + F
  S:     6 QFTVSQKETGSRLDVCLAGRFPEFTRSYLQKLCKDSAVLVDDAEKKSNYKVREGE--RVILK---VPKPTELSIKPEKMDLDIVYEDRDIILINKPKNMVVHPAPGHYEGTLVNGLMEHCRDELSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQCLAEQLKDHTITRRYHAIVCHNIKEESGTVDAPIARSRKDRKKMAIDREA--GRRAVTHYRVLERLKEGFTYIECRLETGRTHQIRVHMASIGHPLLGDTVYGPKKSKYSLEGQCLHAKVLGF 278
>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 = 306, Expect = 3.3e-26, Identities = 80/246 (32%), Positives = 125/246 (50%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLK---DFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           L   ++  F   S ++I K I    + VN K     Y +Q+ D   + +++ P+KK      L  K  L+++YED ++IVVNKP+G++  P       TL N +  +             + HR+DK T+GL + AKN      L+    +    + YL + +G F +K  T+K   D    N +KQ +  +      +E IT ++V+E   + +L+E  L TG+ HQIRVHMA IGHPV GD  Y  +
  S:    22 LDKILATDFSAFSRNQIKKLIDQDRVIVNGKPVLAKYLVQDGD--HVVIKVPPVKKT---ELLPEKIPLDIVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNALLSHAPLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFSEKRGTIKAPIDRDPKNRQKQAVVAN-----GREAITHFKVLESFSNYSLIEAVLETGRTHQIRVHMAYIGHPVAGDPLYGPR 260
>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 = 306, Expect = 3.3e-26, Identities = 84/259 (32%), Positives = 143/259 (55%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVN-HKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKP---ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +++ +  E   + +  +++    E+S S+I + ++ G+I +    +   NY+L+  + +++ L  +P         L A+P    L+++YED++IIVVNKP+G++  P    +  TL N +   LY   D       L   + HRLDK T+G+ VAAKN      L       ++ + YL L +G+  +    ++  I  +  ++Q M +  +N  ++  +T YRV+E      LLE +L TG+ HQIRVHMA IGHPV+GD KY  +
  S:     1 MEVVVPPEARGRRIDAWLAGELPEVSRSRIQQLLEAGEITLALPGRLKANYRLRGGERVRVRLP-EP-------TLLAARPEAIPLDILYEDEDIIVVNKPQGMVVHPAPGSEGGTLVNAL---LYHCGDLSGINGVLRPGIVHRLDKDTSGILVAAKNDAAHRGLAAQIKDHSMKRIYLALVHGEVAEPRGRVEAPIGRHPVDRQRMAVTLKN--SRPAVTHYRVVEHFPGYTLLEARLETGRTHQIRVHMAFIGHPVVGDPKYGPR 255
>gi|160939065|ref|ZP_02086416.1| hypothetical protein CLOBOL_03959 [Clostridium bolteae ATCC BAA-613] >gi|158438028|gb|EDP15788.1| hypothetical protein CLOBOL_03959 [Clostridium bolteae ATCC BAA-613] (366 aa)
Score = 306, Expect = 3.6e-26, Identities = 86/260 (33%), Positives = 149/260 (57%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKK--ELKLNFLEAKP----------------------------------ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEK-----KDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           M  + + + E  Q L   ++K   +     I K ++  +I +N KK   + +L+E D +++FL  + I+K     +   E +P                                   L+++YED++I+VVNKP G++ Q  K+  + +LN  I  YL +            + ++C+RLD+ T+GL VA K+   L  +N ++   ++ KYY CL  G+ K+K   +  F+  +E    + I   E + +  I+T+Y  +   K   LL++ L+TG+ HQIR H+ASIGHP++GD KY  +
  S:     1 MQTLTVTQNEAGQRLDKLLTKYLNQAGKGFIYKMMRKKNITLNGKKCDGSERLEEGDQVKLFLSDETIEKFSVPDMGGYEKQPGDQSSTGASSHEKREKARGKGGEHQGSRDREGGRRLDIVYEDQHILVVNKPSGMLSQKAKDSDM-SLNEYILNYLIDSGKLPISQLRTFKPSICNRLDRNTSGLVVAGKSLAGLQVMNEVFKDRSIHKYYQCLVAGEIKEKQ-LIAGFLKKDESTNTVSIFPLEVEDSVPIMTEYLPLSGNKTFTLLQVTLITGRSHQIRAHLASIGHPIVGDYKYGSR 300
>gi|182417587|ref|ZP_02948909.1| pseudouridine synthase, RluA family [Clostridium butyricum 5521] >gi|182378542|gb|EDT76071.1| pseudouridine synthase, RluA family [Clostridium butyricum 5521] (324 aa)
Score = 306, Expect = 3.7e-26, Identities = 99/289 (34%), Positives = 159/289 (55%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNE-KIDTLNNRIKKYLYEKKDKNYLEAN-------LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++I I   E  Q L  F+ K  K++ LS I K+++  DI+VN KK    Y L+E D ++I   ++  K++    F++  P  + + +ED+N+++V K  G++   D N+ K  TL + +  YL +K D  YL  N        C+RLD+ T+G+ +  K  + L  +N     + V KYY  L  GK K  S   + +I  N E  I  + D+E K +K+I     V+E     + +EI L+TG+ HQIR H+A +G+P++GD KY  K         +G  +  L +YK+ F   K    +  NK
  S:     1 MKIEIGSNEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGKKQNEKYFLEEGDIVEIKY-IQSKKEDKTQKFIKVDPKRMKICFEDENMVIVEKWPGILVHSDTNDNKEPTLTDYVLSYLNDKGD--YLPENEITFTPAACNRLDRNTSGIIMYGKTFEGLKCINEAIREDEVKKYYYTLAKGKVK--SGLYEGYIVKNPETNISTVYDKEVKNSKKIAMDVNVVETNGAYSFVEINLITGRSHQIRAHLAHVGNPIIGDNKYGDKKLNSFFESKYGLNYQYLYAYKLNFRKIKGKLEYLDNK 301
>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 = 306, Expect = 3.8e-26, Identities = 80/246 (32%), Positives = 125/246 (50%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLK---DFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           L   ++  F   S ++I K I    + VN K     Y +Q+ D   + +++ P+KK      L  K  L+++YED ++IVVNKP+G++  P       TL N +  +             + HR+DK T+GL + AKN      L+    +    + YL + +G F +K  T+K   D    N +KQ +  +      +E IT ++V+E   + +L+E  L TG+ HQIRVHMA IGHPV GD  Y  +
  S:    18 LDKILATDFSAFSRNQIKKLIDQDRVIVNGKPVLAKYLVQDGD--HVVIKVPPVKKT---ELLPEKIPLDIVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNALLSHAPLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFSEKRGTIKAPIDRDPKNRQKQAVVAN-----GREAITHFKVLESFSNYSLIEAVLETGRTHQIRVHMAYIGHPVAGDPLYGPR 256
>gi|189499996|ref|YP_001959466.1| pseudouridine synthase, RluA family [Chlorobium phaeobacteroides BS1] >gi|189495437|gb|ACE03985.1| pseudouridine synthase, RluA family [Chlorobium phaeobacteroides BS1] (346 aa)
Score = 305, Expect = 4.5e-26, Identities = 81/244 (33%), Positives = 130/244 (53%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL---YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI--FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           ++++  +  + +K+ ++I    ++VN K    NYK++  DS++I   L+P   EL     E  P+ ++IYED +++V+NK  G++  P       TL N I  +L    EK D   L   + HRLDK T+GL + AK+   L  L   +    V K Y  + +G  +     +K  I   + + K +   D E K  K  +T+YRV+E  +  +L+E+ L TG+ HQIRVH+  I  P+LGD  Y   G
  S:    39 YLAQQVENATRNKVQEAISEHRVRVNGKTVKANYKIKSLDSIEITF-LRPPAPELAP---EDIPV-DIIYEDNDLMVINKAPGMVVHPAFGNWTGTLANAILHHLGTDAEKLDTTELRPGIVHRLDKNTSGLIIVAKHATALHRLAKQFAERQVEKKYQAIVWGVPEPPEGIVKTNIGRSIRDRKVMTSYDFEGKEGKTAVTEYRVVENLRYFSLVEMILHTGRTHQIRVHLKHINAPILGDETYGGAG 282
>gi|150016268|ref|YP_001308522.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB 8052] >gi|149902733|gb|ABR33566.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB 8052] (324 aa)
Score = 305, Expect = 4.6e-26, Identities = 95/276 (34%), Positives = 154/276 (55%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNK-PRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN-------LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKF 277
           ++I I   E  Q L  F+ K  K++ LS I K+++  DI+VN  K    Y LQE D ++I   ++  K++ K  F++  P  + + YED+N++V+ K P  L+     N +  TL + +  YL +K D  Y+  N        C+RLD+ T+G+ +  K  + L  +N     + + KYY  L  GK +  +   + +I  N E    +I D E K +K+I  +  ++E     +LLEI L+TG+ HQIR H+A +G+P++GD KY  K         +G  F  L +YK+ F
  S:     1 MKIEIGPNEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGTKQNEKYFLQEGDVVEIKY-IQSNKEDKKEKFIKVDPKRIKIAYEDENVVVIEKWPDVLVHSDSNNSEEPTLTDYVLSYLNDKGD--YIPENEITFTPAACNRLDRNTSGMVMFGKTFEGLKAINEAIREDEIRKYYYALAKGKIR--AGLYEAYILKNPETNTSKIYDTEVKNSKKISMEISIVESNGAYSLLEIHLITGRSHQIRAHLAHLGNPIIGDNKYGDKKLNSFFESKYGLNFQYLYAYKLNF 288
>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 = 304, Expect = 6.1e-26, Identities = 87/274 (31%), Positives = 148/274 (54%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKP-IKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF-GFQFPCLTSYKIKFNFDKN 282
           E   + L  +I++    LS S I + + +G I VN++    + +L+  D++ I   + P    ELK    E  P L +I++DK+++++NKP GL   P       TL N +     E +D  + L   + HRLDK T+GL + AKN++ L  L+  +    V KYYL L  G+ +     ++  +  + + +Q + +  + +  +   T Y+V+   +  +LLE++L TG+ HQIRVH A+IGHPV GD  Y +K ++   QF  L ++++ F    N
  S:     9 ETAGERLDKYITQKESGLSRSFIQELVSSGHILVNNQSAKPSLRLKTGDTITI--EIPPETPSELKA---ENIP-LEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLALEPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTVRKYYLALVKGELRPAEGFIEAPLGRDPQNRQKIAVVSDGRHAR---TGYKVLRYIQGYSLLEVKLETGRTHQIRVHFAAIGHPVAGDAVYGQKESWVKRQF--LHAHRLSFALPSN 275
>gi|153814854|ref|ZP_01967522.1| hypothetical protein RUMTOR_01069 [Ruminococcus torques ATCC 27756] >gi|145847885|gb|EDK24803.1| hypothetical protein RUMTOR_01069 [Ruminococcus torques ATCC 27756] (347 aa)
Score = 304, Expect = 6.1e-26, Identities = 90/277 (32%), Positives = 150/277 (54%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKK----------ELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL----YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKE---IITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKF 277
           M +I I   E  Q    F+ K   +   S + K ++  +I +N KK   N  L   D++++F   + IKK           ++ N  ++K  LNV+YED+N+I +NKP G++ Q    E    +   I+  L      +++       +C+RLD+ T+G+    K    L  LN ++ T ++ KYYLCL  GK K     +  ++  N +   + + +E +  KE   I T+Y  +     + LL++ L+TGK HQIR H+A+IGHP++GD KY         K  +G +   L +Y++ F
  S:     1 MKEIEINSNEAGQRFDKFLGKYLDQAPKSFLYKMLRKKNITLNGKKAAGNEILALGDNVKLFFSDETIKKFSKTSEEVFRPVQKNTAKSKVKLNVLYEDENVIFLNKPVGMLSQKANREDTSLVEYLIEYLLDSGQVTREELKTFHPAVCNRLDRNTSGIVAGGKTLSALQILNEMFRTRSLEKYYLCLVSGKIKD-GQRICGYLKKNTKTNKVSVTKEKRETKEALPIETEYTPLFVSDHVTLLKVHLITGKTHQIRAHLAAIGHPIIGDYKYGDFKINEAYKKKYGLKTQLLHAYQLCF 300
>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 = 303, Expect = 6.7e-26, Identities = 85/252 (33%), Positives = 136/252 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIE-------QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I  E E++ +  F+++  + +S S I K IK+  +K+N      NY+L+E D L        + + + L        L+++YED++IIV+NKP+GL+  P       TL N +   LY  KD+       +   + HR+D  TTG+ V  KN K+   +       ++++ Y  L Y  FK+   T+   I  +  +++ M I+ +N   K  +T YRV+E         +  A +E  L TG+ HQIRVHMAS+ HP+LGD  Y
  S:     9 IDSEYEDERIDSFLAEFEEGISRSYIQKLIKDSLVKINGNVIKANYRLKEGDILTY-----EVPQPVSLEIAAENIPLDILYEDEDIIVINKPKGLVVHPAAGHYSGTLVNAL---LYHCKDRLSGINGVMRPGIVHRIDMNTTGVLVVCKNDKSHQSIAEQLKVHSITRKYEALVYNSFKQTEGTVDAPIGRHPVDRKKMAINHKN--GKNAVTNYRVLENFNLGYVHNQGYAHIECTLKTGRTHQIRVHMASLHHPLLGDDVY 263
>gi|3915406|sp|O50310|YBC5_CHLVI Uncharacterized RNA pseudouridine synthase in bchI 5'region (RNA-uridine isomerase) (RNA pseudouridylate synthase) >gi|2661852|emb|CAB06297.1| hypothetical protein [Prosthecochloris vibrioformis] (327 aa)
Score = 302, Expect = 8.7e-26, Identities = 83/284 (29%), Positives = 145/284 (51%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL---YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEE--KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKFK 301
           ++++  + ++ +K+  +I+ G + VN K    NY+++  D + +   L+P   EL     E  PI  ++YED +++V++K  G++  P       TL N I  +L    ++ DK  +   + HRLDK T+GL + AKN   L +L   +    V K Y  + +G  K +S T+K  I  + +  K +     E    K  IT Y+V+E     +L+++ L TG+ HQIRVH+  +GH +LGD  Y      G   P    +     F +N  L  +++  L  + ++F+
  S:    17 YLTQQVENMTRNKVQAAIEEGRVLVNGKPVKSNYRVKSCDHIHLTF-LRPPAPELAP---EDIPI-TILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHLGKDADELDKTEMRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVEKVYKAIVWGVPKAESGTIKTNIGRSHKNRKVMANFPYEGAEGKHAITDYQVVEDLGYFSLMDVTLHTGRTHQIRVHLQHLGHSILGDETY------GGATPRTLPFSKSEPFTRN-LLELMSRQALHAQTLRFR 293
>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 = 302, Expect = 9.2e-26, Identities = 84/262 (32%), Positives = 146/262 (55%)
  Q:    21 KSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN 282
           K++ + S   I K+ + G IKVN++    +Y L+ ND ++I      I ++ + + +  K  L++IYED++IIV+NKP+ ++  P K     TL+N +  Y  EK + + +   L +RLD  T+GL + AKN  +   L+     +   K YL + +G  ++KS  +   I+   E  +  +  E    ++ IT+++VIE  ++  L+E+ L TG+ HQIRVH++SIGHP+ GD  Y K+ +       L +YK++    K+
  S:    26 KNYAKCSSRFIRKAAREGRIKVNNENVRLSYMLKNNDLIEI-----QINRKEEQDIVPEKMKLDIIYEDEDIIVINKPKAIVVHPTKRHLNGTLSNGVLYYFKEKNENSIVR--LVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFIKRYLAIVHGNLEEKSGVIDKPIYRVGEGTLKRVIDER--GQKSITRFKVIESYENADLIELTLETGRTHQIRVHLSSIGHPIYGDALYGKEEHEYIDRQALHAYKLQIPHPKD 278
>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 = 302, Expect = 9.5e-26, Identities = 87/274 (31%), Positives = 146/274 (53%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKP-IKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN 282
           E + + L  +I++   +LS S I   I +G ++VN K    + KL+  D++ I   + P    ELK    E  P L +I++DK+++++NKP GL   P       TL N +     + +D  + L   + HRLDK T+GL + AKN++TL  L+  +    V KYYL L  G+       ++  +  + + +Q + +    +  +   T Y+V+   +  +LLE++L TG+ HQIRVH A+IGHPV GD  Y +K  +  +   L ++++ F    N
  S:     9 ESDGERLDKYIAQKETDLSRSFIQALIDSGHVQVNGKTAKPSLKLKNGDTITI--EISPETPPELKA---EDIP-LEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLINGVLALEPKMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRETLANLSAQFKERTVRKYYLTLVKGELHPAEGFIEAPLGRDPQNRQKIAVVSNGRHAR---TGYKVLRYIQGYSLLEVKLETGRTHQIRVHFAAIGHPVAGDAIYGQKETW-LKRQFLHAHRLSFTLPSN 275
>gi|49066398|gb|AAT49291.1| putative bacteriocin [Prevotella nigrescens] (363 aa)
Score = 302, Expect = 1.0e-25, Identities = 84/255 (32%), Positives = 133/255 (52%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKK--DKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++ + K +E   +  F+ +  +  S ++I K+   G I VN      NYK++ ND + + L  +P  K       E  P LNV+YED  I+V+NKP GL+  P       TL N I  +L + K  D N     L HR+DK T+GL + AK     T L   +  +   + Y+ L +G F +    ++  I  + + ++ M++ D ++   K  +T Y+V+E+     L+E  L TG+ HQIR HM  IGHP+ GD +Y
  S:    35 RVEVDKGQEAVRIDKFLFERMQHSSRNRIQKAADAGSIYVNGTPVKSNYKVRPNDVITLMLD-RP--KHDNTIVAEDMP-LNVVYEDNEIMVINKPAGLVVHPGAGNFRGTLINAIAWHLRDLKNFDPNDPAVGLVHRIDKDTSGLLLIAKTPDAKTFLGKQFFNKTTHRSYVALVWGNFTEDEGRIEGNIGRDSKDRLRMKVFDTDSGIGKPAVTHYKVLERFGYTTLIECILETGRTHQIRAHMKHIGHPLFGDERY 289
>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 = 301, Expect = 1.1e-25, Identities = 86/274 (31%), Positives = 148/274 (54%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKP-IKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF-GFQFPCLTSYKIKFNFDKN 282
           E   + L  +I++    LS S I + + +G I VN++    + +L+  D++ I   + P    ELK    E  P L +I++DK+++++NKP GL   P       TL N +     E +D  + L   + HRLDK T+GL + AKN++ L  L+  +    + KYYL L  G+ +     ++  +  + + +Q + +  + +  +   T Y+V+   +  +LLE++L TG+ HQIRVH A+IGHPV GD  Y +K ++   QF  L ++++ F    N
  S:     9 ETAGERLDKYITQKESGLSRSFIQELVSSGHILVNNQSAKPSLRLKTGDTITI--EIPPETPSELKA---EDIP-LEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLALEPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTIRKYYLALVKGELRPAEGFIEAPLGRDPQNRQKIAVVSDGRHAR---TGYKVLRYIQGYSLLEVKLETGRTHQIRVHFAAIGHPVAGDAVYGQKESWVKRQF--LHAHRLSFALPSN 275
>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 = 301, Expect = 1.2e-25, Identities = 87/274 (31%), Positives = 147/274 (53%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKP-IKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN 282
           E + + L  +I++   +LS S I + ++ G I+VN K    + KL+  D++ I   + P    ELK    E  P L +I++DK+++++NKP GL   P       TL N +     E +D  + L   + HRLDK T+GL + AKN++ L  L+  +    V KYYL L  G+       ++  +  + + +Q + +    +  +   T Y+V+   +  +LLE++L TG+ HQIRVH A+IGHPV GD  Y +K  +  +   L ++++ F+   N
  S:     9 ESDGERLDKYITQKETDLSRSFIQELVEAGHIQVNGKNAKPSLKLKNGDTITI--EIPPETPPELKA---EDIP-LEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLINGVLALEPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNREALANLSAQFKERTVRKYYLTLVQGELHPAEGFIEAPLGRDPQNRQKIAVVSNGRPAR---TGYKVLRYIQGYSLLEVKLETGRTHQIRVHFAAIGHPVAGDAVYGQKETW-LKRQFLHAHRLSFSLPSN 275
>gi|193212389|ref|YP_001998342.1| pseudouridine synthase, RluA family [Chlorobaculum parvum NCIB 8327] >gi|193085866|gb|ACF11142.1| pseudouridine synthase, RluA family [Chlorobaculum parvum NCIB 8327] (349 aa)
Score = 301, Expect = 1.3e-25, Identities = 83/284 (29%), Positives = 145/284 (51%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL---YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEE--KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKFK 301
           ++++  + ++ +K+  +I+ G + VN K    NY+++  D + +   L+P   EL     E  PI  ++YED +++V++K  G++  P       TL N I  +L    ++ DK  +   + HRLDK T+GL + AKN   L +L   +    V K Y  + +G  K +S T+K  I  + +  K +     E    K  IT Y+V+E     +L+++ L TG+ HQIRVH+  +GH +LGD  Y      G   P    +     F +N  L  +++  L  + ++F+
  S:    39 YLTQQVENMTRNKVQAAIEEGRVLVNGKPVKSNYRVKSCDHIHLTF-LRPPAPELAP---EDIPI-TILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHLGKDADELDKTEMRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVEKVYKAIVWGVPKAESGTIKTNIGRSHKNRKVMANFPYEGAEGKHAITDYQVVEDLGYFSLMDVTLHTGRTHQIRVHLQHLGHSILGDETY------GGATPRTLPFSKSEPFTRN-LLELMSRQALHAQTLRFR 315
>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 = 301, Expect = 1.4e-25, Identities = 89/273 (32%), Positives = 145/273 (53%)
  Q:     5 FIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
            +  +EEN  L  FI K  ++ S S I   I++  ++VNH+    NYK +  D++++ L   P   EL +   + K  L+++YED ++IVVNKP+G+I  P       TL N +  +  E            + HR+DK T+G+ V AKN  +  +L+      ++++ Y+ L  G  K++  +L   I  +++ +I     E    K  +T Y VI++ K+  L++  L TG+ HQIRVHM  +GHPV+GD  Y  KK  F  +   L + K+ F
  S:     7 LVNDDEENLRLDLFICKHIQDKSRSYIQNLIEDNLVEVNHRMKKSNYKTKTGDNIKVSL---PDAVELNIKGEDIK--LDILYEDSDVIVVNKPQGMIVHPASGVYTGTLVNALLNHCREDLSGINGIARPGIVHRIDKDTSGILVIAKNDMSHNKLSEQLKDHSMTREYIALVEGIIKEEKGSLDKPIGRHKKDKIKMAVVEG--GKRAVTHYEVIKRFKEYTLVKCILETGRTHQIRVHMCYLGHPVVGDPVYGYKKQKFNLKGQLLHAQKLGF 275
>gi|119357434|ref|YP_912078.1| ribosomal large subunit pseudouridine synthase D [Chlorobium phaeobacteroides DSM 266] >gi|119354783|gb|ABL65654.1| ribosomal large subunit pseudouridine synthase D [Chlorobium phaeobacteroides DSM 266] (350 aa)
Score = 301, Expect = 1.4e-25, Identities = 85/243 (34%), Positives = 131/243 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANL-----CHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEE--KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +  ++++  +  + +K+ ++I  G + VN K    NYK++  D +QI   L+P   E+     E  PI ++IYED +++VVNK  G++  P       TL N I  ++    D   L+ +L      HRLDK T+GL + AKN   L  L   +    V K Y  L +G  +  S T+K  I  +++  K +     E    K  IT Y VIE  +  +L+ I+L TG+ HQIRVH+  +GHP+LGDT Y
  S:    36 IDKYLTQQVENATRNKVQEAITEGRVLVNGKPVKSNYKIKSCDLIQITF-LRPPAPEMAP---ENIPI-DIIYEDADLMVVNKEAGMVVHPAFGNWTGTLANAILHHI--GNDTGELDCSLQRPGIVHRLDKDTSGLIIIAKNPLALQRLARQFAQRQVEKIYHALVWGVPEPASGTIKTNIGRSKKNRKVMTTYPFEGIDGKHAITDYAVIEDLRYFSLVSIKLHTGRTHQIRVHLQHLGHPILGDTVY 278
>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 = 300, Expect = 1.5e-25, Identities = 97/293 (33%), Positives = 156/293 (53%)
  Q:     5 FIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEA----NLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNF-----------GFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKN 297
            I +E+ N  L   I+   +ELS ++I   I  G + VN KK   +YK + ND ++I      I   + L+       L ++YED+++IVV+KP G+I  P       TL N +   L+  KD + +       + HR+DK T+GL + AKN      L+       V + Y+ L +G    +   +   I  N +++Q M + R N  +KE +T + V+++   M+L+E +L TG+ HQIRVHM+ IG+PV GD KY  +K +F           GF  P    Y    +   ++F   L++L  E+K+
  S:     6 LIIEEDNNLRLDKVIAMQLQELSRTQIQDMINQGLVLVNQKKEKASYKTKLNDEIEI-----TILDNVDLDIEPEDISLKIVYEDEDVIVVDKPTGMIVHPSAGIMHGTLVNAL---LFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDNAHRLLSKQLKDHTVVRRYVALVHGLIPHEHGKVDAPIGRNPKDRQSMAVTRTN--SKEAVTNFTVLKRYNAMSLIECRLETGRTHQIRVHMSYIGYPVYGDPKYGYRKDDFSHGQFLHAKKLGFIHPTTQKYMEFESPLPDYFQAKLDELQEELKD 305
>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 = 300, Expect = 1.9e-25, Identities = 83/259 (32%), Positives = 134/259 (51%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++  I +E   + L   +S   +ELS S+  + IK+G I VN + T  NYK   +D ++I     P  +EL  + L  +  L++ YED +++VVNKP+G++  P       TL N +  +  +    N  L   + HR+DK T+GL + AKN      L N    + V++ Y  + +G       T+   +  + +++Q M +       K  +T + VI + KD   +E QL TG+ HQIRVHM  IG+P+ GD KY  +
  S:     4 MEYIINEEVAGERLDKAVSLLNEELSRSQAQQMIKDGHILVNGQGTKTNYKCSIDDKIEISF---PEPEEL--DVLPEEMDLDIYYEDGDVLVVNKPKGMVVHPAPGHASGTLVNGLMAHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRKYQAIVHGTIPHDYGTVDAPLGRDPKDRQSMTV---VDGGKHAVTHFHVIHRYKDFTHVECQLETGRTHQIRVHMKYIGYPLAGDPKYGPR 256
>gi|153954106|ref|YP_001394871.1| RluD2 [Clostridium kluyveri DSM 555] >gi|146346987|gb|EDK33523.1| RluD2 [Clostridium kluyveri DSM 555] (319 aa)
Score = 299, Expect = 2.5e-25, Identities = 93/295 (31%), Positives = 157/295 (53%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVK 296
           +++ I   E  Q L  F+ K  +++ +S I K+I+ GDIKVN KKT   Y L + D ++    +    K  + N + +   L + YED+N+I+V K  G++   DK     TL + +  YLY+K D     +     + C+RLD+ T+G+ +  KN ++L  LN +     + KYY  L  G+  +     + +I  + +  I  + D   K  K+I    +V+      +L E++L+TG+ HQ+R H+A +G+P++GDTKY            +G  +  L +YK+ F  D N  L Y+N   +  K
  S:     1 MKVEIGSNESGQRLDKFLRKWLRDVPISGIYKAIRKGDIKVNGKKTKEKYFLMDKDIVEAQYIISK-GKSFEFNKVNSN-FLKITYEDENMILVEKWPGVLVHSDKKTDDVTLTDYVLSYLYDKGDFKPETEVTFTPSPCNRLDRNTSGIVIYGKNYESLKLLNEIIRERNIRKYYQALVKGRINE--GIYEGYILKDRKNNISNVYDSPKKNTKKISMDVKVLHTCGTYSLAELELITGRSHQLRTHLAHLGNPIIGDTKYGISKINSFFYNKYGLTYQYLYAYKVIFK-DCNGKLSYMNNKTISEK 303
>gi|196177833|gb|EDX72836.1| pseudouridine synthase, RluA family [Microcoleus chthonoplastes PCC 7420] (330 aa)
Score = 298, Expect = 2.5e-25, Identities = 82/268 (30%), Positives = 137/268 (51%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKK-TTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           M +I +  +E +  L  ++++   +LS S+I K I+ G++++NH   T+    +Q  DS+ + +   P  K L L   EA P L+++YED  I++VNKP  L+  P    +  TL N +  +         ++   + HRLDK TTG    AK       L      +   + YL + YG    ++ T+   I  +  +++ M +    K  +  IT +++ E+  +  L+  QL TG+ HQIRVH A IGHP++GD  Y+K  + G   P
  S:     1 MKEINLYNQENSDRLDRYLAQQLPDLSRSRIQKLIEEGNVQLNHNLCTSKKATIQPGDSIHLTI---PDAKPLDLK-PEAIP-LDILYEDDQILIVNKPANLVVHPAPGHENGTLVNALLAHCPNLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDHAHHHLQAQLKAKTARRDYLGVVYGSPATETGTINFPIGRHPSDRKKMAVVPLEKGGRSAITHWQIKERLGNYTLIHFQLETGRTHQIRVHTAHIGHPIIGDPVYSKGRDIGVNLP 266
>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 = 298, Expect = 2.6e-25, Identities = 86/255 (33%), Positives = 146/255 (57%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++KE +N  L  ++SK F++ S S +   I  G++ VN+K+   NYKL+  D++++ +       E KL  +E + I L++IYEDK++IVVNKP+ ++  P       TL N +  +  +    N +    + HR+DK T+G+ V AKN  +   L   +   ++S+ Y+ L  G  K    T++  I  +   +I M + ++ ++    +T Y+VIE+ K+  L+E +L TG+ HQIRVHM+ I HP++GD  Y  K
  S:     8 VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIKVNI------PEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLSHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDGQGTIEAPIGRHPVDRIKMAVVKDGRY---AVTHYKVIERFKNHTLVECKLETGRTHQIRVHMSHIMHPLVGDPVYGYK 256
>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 = 298, Expect = 2.8e-25, Identities = 96/272 (35%), Positives = 147/272 (54%)
  Q:     6 IKKEEENQILKDFI-SKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQL-LTGKKHQIRVHMASIGHPVLGDTKYNKKGN---FGFQFPCLTSYKIKF 277
           ++K EE   L  F+  K+   +S S I K+IK G +KVN +    +YKL+E + +++ L  KP +  ++   +E    L V+YED++IIV++KP  +I  P  ++   TL N +   L+  KD       L   + HRLDK T+G+ V AKN      L+  +    V K Y+ L  GK K     +   +  +   +I     E    KE IT+YRV+++  D+A L +    TG+ HQIRVHM S+GHP++GD  Y K      FG +   L + K+ F
  S:     6 VEKREEGWRLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEVDLPEKPQEATVQPEEIE----LKVLYEDRDIIVIDKPGDMIVHPVPSKLSGTLVNAL---LHHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYILLVKGKMKNDEGVIDLPLARHPVLRIKMAVVET--GKEAITEYRVLKRFDDVATLVLAFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEIFGIKRQMLHALKLGF 277
>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 = 298, Expect = 2.9e-25, Identities = 74/248 (29%), Positives = 143/248 (57%)
  Q:    10 EENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           E++  +  +++++  +LS S I K +K+G + VN +    +Y + E+D +++ +  + ++ E+     +A+P+ L+++YED+++I++NKP+G++  P       TL N +   +Y  KD+       +   + HR+D  TTG+ +A KN    + +       ++++ Y  + +G   +   T+   I  +  E++ M I+ +N   K  +T YRV+ + +    +E +L TG+ HQIRVHMASI HP+LGD  Y
  S:     2 EDHVRIDKYLAEACPDLSRSYIQKLLKSGQVLVNGQGIKASYIVVEDDRIELEVP-EAVEPEI-----DAEPMDLDILYEDQDLILINKPKGMVVHPAAGHYSHTLVNGL---MYHCKDQLSGINGVMRPGIVHRIDMDTTGVIIACKNDMAHSSIAAQLKEHSITRRYQAIVHGVIAEDEGTVDAPIGRHPVERKKMSINYQN--GKNAVTHYRVLNRFRQYTHVECRLETGRTHQIRVHMASIRHPLLGDAVY 245
>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 = 298, Expect = 3.2e-25, Identities = 92/272 (33%), Positives = 150/272 (55%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           I++E ENQ +  ++++ F+ +S S I   I    + VN K    NYKL+  D+++  +   P  +ELK+   EA+ I L+++YED++I+VVNK +G++  P       TL N +   LY  KD       L   + HR+DK T+G+ V AKN      L N     ++++ Y  +  G  K+   T+   +  +  E  +I  +    K  +  +T Y+V+E+ ++  L+E +L TG+ HQIRVHMA IGH ++GD  Y  KK  F  +   L + K+ F
  S:     8 IEEEYENQRIDVYLAQEFENISRSHIQDLIGKKKVFVNGKAVKSNYKLKSRDNVEFEI---PDNEELKI---EAENIPLDIVYEDRDIVVVNKAQGMVVHPAPGNYNGTLVNAL---LYHCKDLSGINGVLRPGIVHRIDKDTSGILVVAKNDAAHKNLANQLKEHSMNRVYRAVVEGIIKEDEGTVDKPLARHPVERVKIAVV----KGGRNAVTHYKVLERYRNSTLIECKLETGRTHQIRVHMAYIGHALVGDPLYGYKKQRFNLEGQMLHAQKLGF 274
>gi|160880920|ref|YP_001559888.1| RluA family pseudouridine synthase [Clostridium phytofermentans ISDg] >gi|160429586|gb|ABX43149.1| pseudouridine synthase, RluA family [Clostridium phytofermentans ISDg] (346 aa)
Score = 297, Expect = 3.4e-25, Identities = 93/275 (33%), Positives = 159/275 (57%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKP-----ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE-----KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKE---IITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY-----NKK--GNFGFQFPCLTSYKIKF 277
           +I I + E  Q L  F++K   +   S   K ++  +I +N KK     KL E D +++FL  + I+   +   L+AK       L+V+YED +++++NKP G++ Q  K   + +L   +  YL E     K++ +  + ++C+RLD+ T+G+ +A K+   L E++      ++ KYY C+  G   K +  +  ++  +E+   + I   +  + E   I T+Y+ I  K    LLE+ L+TGK HQIR H++SIGHP++GDTKY     NKK    +G     L SY+++F
  S:    20 EITIVQNEAGQRLDKFLAKYLNKAPKSFFYKMLRKKNITLNGKKAEGAEKLIEGDIVRLFLAEETIESFKESYQLDAKVNQRAVKLDVLYEDSHVVIINKPIGMLSQRAKESDV-SLVELLIAYLLEMGSLTKEELSTFKPSVCNRLDRNTSGIVIAGKSLLGLQEMSAKLQDRSLHKYYRCIVKGTMTKGA-RINGYLAKDEKTNKVRITTNDPNDGESSYIETEYQPILSKNGYTLLEVLLITGKTHQIRAHLSSIGHPIIGDTKYGDETLNKKMQKQYGLSHQLLHSYRLEF 312
>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 = 297, Expect = 3.6e-25, Identities = 87/267 (32%), Positives = 140/267 (52%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD---KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYK 274
           K +E   +  F+    +  + +KI ++ K+G I VN K    NYK++  D +++     P   EL L   E  P L+++YED  ++VVNKP G++  P       TL N +   LY  KD    +     L HR+DK T+GL V AK +  +T L   +  +   + Y+ L +G  + +S T++  I  N + ++ M++  E +  KE +T Y V+E+   + L+  +L TG+ HQIRVHM  IGH +  D +Y   G+   +    T YK
  S:    24 KGQEPLRVDKFLMNFIENATRNKIQQAAKDGHIWVNEKIVKQNYKVKAGDEVKVLFEHPPY--ELLLT-PENIP-LDIVYEDDVLLVVNKPAGMVVHPGHGNYTGTLINAL---LYHSKDLPVNSNDRPGLVHRIDKDTSGLLVVAKTEAAMTHLAKQFFDKTSEREYVALVWGNVEDESGTIEGNIARNPKNRLQMQVFPEGEQGKEAVTHYGVLERLGYVTLVSCKLETGRTHQIRVHMKYIGHTLFNDERYG--GDKVLKGTTFTKYK 285
>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 = 297, Expect = 3.6e-25, Identities = 85/263 (32%), Positives = 141/263 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFL------RLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-------------KKGNFGFQFP 268
           +++E+E   L  F++    ELS ++I K I    + VN +    +++++  D +++ +      R++P          EA P L V +ED +++VVNKPRGL+  P       TL N +  +  +    N  L   + HRLD+ T+GL + AKN      L       AV + Y  L +G+ ++++ T+   I  +  ++Q M +   +   +   T YRV+ +    +LLE+ L TG+ HQIRVHMA +GHP++GD KY                G  GF+ P
  S:     9 VEEEDEQTRLDVFLAGQNPELSRARIQKLISLELVTVNGRPARASHRVRGGDCVELKVPDPETPRIEP----------EAIP-LEVCFEDPDVLVVNKPRGLVVHPAVGHYSGTLVNALLHHCRDLSGINGILRPGIVHRLDRDTSGLLMVAKNDAAHLALAGQLKDRAVLRRYTALVHGRPRRETGTVDAPIGRHPRDRQRMAVTPRS--GRAARTHYRVVRRFDKFSLLELTLDTGRTHQIRVHMAHVGHPLVGDLKYGHARPELGLEGQFLHAGTLGFRHP 279
>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 = 297, Expect = 3.7e-25, Identities = 87/259 (33%), Positives = 148/259 (57%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I + ++KE +N  L  ++SK F++ S S +   I  G++ VN+K+   NYKL+  D++++ +       E KL  +E + I L++IYEDK++IVVNKP+ ++  P       TL N +  +  +    N +    + HR+DK T+G+ V AKN  +   L   +   ++S+ Y+ L  G  K +  T++  I  +   +I M + ++ +     +T Y+VIE+ K+  L+E +L TG+ HQIRVHM+ I HP++GD  Y  K
  S:     4 INLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIEVNI------PEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQGTIEAPIGRHPVDRIKMAVVKDGR---HAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYK 256
>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 = 297, Expect = 3.8e-25, Identities = 87/259 (33%), Positives = 148/259 (57%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I + ++KE +N  L  ++SK F++ S S +   I  G++ VN+K+   NYKL+  D++++ +       E KL  +E + I L++IYEDK++IVVNKP+ ++  P       TL N +  +  +    N +    + HR+DK T+G+ V AKN  +   L   +   ++S+ Y+ L  G  K +  T++  I  +   +I M + ++ +     +T Y+VIE+ K+  L+E +L TG+ HQIRVHM+ I HP++GD  Y  K
  S:     4 INLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVRDNIEVNI------PEPKLLQIEPEDINLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQGTIEAPIGRHPVDRIKMAVVKDGR---HAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYK 256
>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 = 297, Expect = 4.0e-25, Identities = 87/260 (33%), Positives = 139/260 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFL-RLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK----KGNFGF 265
           ++ E E   L  FIS+   +LS +++ + +K  +I VNHK    +YK+Q  D ++I +  +KP      L+ +     L+++YED+ +IVVNKP+G++  P       TL N +   LY  +D           + HR+DK T+GL + AKN K    L +    +   + Y  + +G F +++  +   I  N   +      EN   K+ +T ++V++Q K  +L+E QL TG+ HQIRVH+  IGH V GD  Y      KGN  F
  S:     7 LQVENEYGRLDKFISEQIPDLSRTRVKELVKEKEILVNHKVEKVSYKIQAGDKIEINVPAVKP------LDVVPENIPLDIVYEDEVVIVVNKPQGMVVHPAPGHPDHTLVNAL---LYHTQDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKRIYWAIVHGDFGEENGVIDAPIGRNPYDRKKMAVVEN--GKKAVTHFKVLKQFKGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGNGQF 264
>gi|15894302|ref|NP_347651.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824] >gi|15023925|gb|AAK78991.1|AE007617_3 Pseudouridylate synthase [Clostridium acetobutylicum ATCC 824] (318 aa)
Score = 296, Expect = 5.0e-25, Identities = 92/276 (33%), Positives = 150/276 (54%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKK-TTWNYKLQENDSLQI-FLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN------KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKF 277
           ++I I   E  Q +  FI K  K++ LS I K+ + GD+ +N  K     Y L+E D L+I ++R    KK+    F   +    V YED+N+++V K  G++   DK +   TL + +  YLY+K D     +     + C+RLD+ T+G+ +  KN + L  LN +     + KYY  L  GK       +KD I+    K+ +  ++    N      K+I  + + +E     + +EI+LLTG+ HQ+R H++ +G+P+LGD KY  K         FG  +  L +YK+ F
  S:     1 MKIVIGPNEAGQRVDKFIRKWLKDVPLSAIYKAFRKGDVIINGAKCKKEKYSLEEGDVLEIKYIRSDAKKKK----FTRIENNFKVTYEDENMLLVEKWPGVLVHSDKEKTSPTLTDYVLSYLYDKGDYAPENEVTFTPSPCNRLDRNTSGIVIYGKNFEALKCLNEMIRERRIKKYYYALVKGK-------IKDGIYEAYIKKDVSSNKSEIINTPAPGAKQISMEIKCVETCGTFSFIEIELLTGRSHQLRAHLSHLGNPILGDPKYGIKDINSYFENKFGLNYQFLYAYKLIF 285
>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 = 296, Expect = 5.2e-25, Identities = 87/259 (33%), Positives = 148/259 (57%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I + ++KE +N  L  ++SK F++ S S +   I  G++ VN+K+   NYKL+  D++++ +       E KL  +E + I L++IYEDK++IVVNKP+ ++  P       TL N +  +  +    N +    + HR+DK T+G+ V AKN  +   L   +   ++S+ Y+ L  G  K +  T++  I  +   +I M + ++ +     +T Y+VIE+ K+  L+E +L TG+ HQIRVHM+ I HP++GD  Y  K
  S:     4 INLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIEVNI------PEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKYEQGTIEAPIGRHPVDRIKMAVVKDGR---HAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYK 256
>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 = 295, Expect = 6.0e-25, Identities = 92/272 (33%), Positives = 147/272 (54%)
  Q:     6 IKKEEENQILKDFI-SKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQL-LTGKKHQIRVHMASIGHPVLGDTKYNKKGN---FGFQFPCLTSYKIKF 277
           ++K EE   L  F+  K+   +S S I K+IK G +KVN +    +YKL+E + +++ L  KP +  ++   +E    L V+YED++I+V++KP  +I  P  ++   TL N +  +  + +     L   + HRLDK T+G+ V AKN      L+  +    V K Y+ L  G+ KK    +   +  +   +I     E    KE IT+YRV+++  D+A L +    TG+ HQIRVHM S+GHP++GD  Y K      FG +   L + K+ F
  S:     6 VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEVDLPEKPQEATVQPEEIE----LKVLYEDRDIVVIDKPGDMIVHPVPSKLSGTLVNALLNHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYILLVKGRVKKDEGVVDLPLARHPVLRIKMAVVET--GKEAITEYRVLKRFDDVATLVLAFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEIFGIKRQMLHALKLGF 277
>gi|21674122|ref|NP_662187.1| ribosomal large subunit pseudouridine synthase D [Chlorobium tepidum TLS] >gi|21647279|gb|AAM72529.1| ribosomal large subunit pseudouridine synthase D [Chlorobium tepidum TLS] (329 aa)
Score = 295, Expect = 6.1e-25, Identities = 78/240 (32%), Positives = 126/240 (52%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL---YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEE--KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++++  +  + +K+ K+I+   + VN K    NY+++  D + I   L+P   EL     E  PI +++YED +++V++K  G++  P       TL N I  +L    +  DK  +   + HRLDK T+GL + AKN   L +L   +    V K Y  + +G     S T+K  I  + +  K +     E    K  IT Y V+E     AL+++ L TG+ HQIRVH+  +GHP+LGD  Y
  S:    17 YLTQQVENATRNKVQKAIEEQRVLVNGKPVKSNYRIKSCDHIHITF-LRPPAPELAP---EDIPI-SILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHLGKDADDLDKTEMRPGIVHRLDKDTSGLIIVAKNPVALHKLATQFARRQVEKVYKAIVWGVPNPPSGTIKTNIGRSHKNRKVMANFPFEGAEGKHAITDYLVVEDLAYFALMDMTLHTGRTHQIRVHLQHLGHPILGDQTY 256
>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 = 295, Expect = 7.0e-25, Identities = 94/272 (34%), Positives = 147/272 (54%)
  Q:     6 IKKEEENQILKDFI-SKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQL-LTGKKHQIRVHMASIGHPVLGDTKYNKKGN---FGFQFPCLTSYKIKF 277
           ++K EE   L  F+  K+   +S S I K+IK G +KVN +    +YKL+E + +++ L  KP +  ++   +E    L V+YED++I+V++KP  +I  P  ++   TL N +   L+  KD       L   + HRLDK T+G+ V AKN      L+  +    V K Y+ L  G+ K     +   +  +   +I     E    KE IT+YRV+++  D+A L +    TG+ HQIRVHM S+GHP++GD  Y K      FG +   L + K+ F
  S:     6 VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEVDLPEKPQEATVQPEEIE----LKVLYEDRDIVVIDKPGDMIVHPVPSKLSGTLVNAL---LHHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYILLVKGRVKSDEGVIDLPLARHPVLRIKMAVVET--GKEAITEYRVLKRFDDVATLVLAFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEIFGIKRQMLHALKLGF 277
>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 = 294, Expect = 7.6e-25, Identities = 82/275 (29%), Positives = 142/275 (51%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           Q  + +++    +   +++   + S S+I   I  G ++VN      NYK  E D+L   +       E K   LE + I L+V+YED ++IV+NKP+G++  P    +  TL + +  +  +    N +E   + HR+DK T+GL V AKN     +L++    + + + Y+ + +G+    +  +   I  + +++Q M +    K     IT +RVIE+  D   +E QL TG+ HQIRVHM  IG P++GD KY+++         L + +I F
  S:     5 QHIVTEQQGKTRVDKLLTQLLADQSRSQIQGWIDEGLVEVNGVSVKANYKCVEGDALTWEI------PETKPLILEPENIPLDVVYEDSDVIVINKPKGMVVHPSAGHQTGTLVHALLYHCDDLSGINGIERPGIVHRIDKDTSGLLVVAKNDVAHQKLSDQLQQKQLKRKYVAIVHGEIGHDTGLIDAPIGRDPKDRQKMAVVDNGK---SAITHFRVIERFPDYTFVECQLETGRTHQIRVHMQYIGFPLVGDPKYSQRKTMNVDGQALHAKEIGF 273
>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 = 294, Expect = 7.7e-25, Identities = 92/286 (32%), Positives = 148/286 (51%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFPCLTSYKIKFNFDKNHFLHYLNKL 291
           I++ +  Q +   +S   K+ S S++   IK G +KVN K    NYK++ ND + +    + ++ ++K   L     L++ YED+++ +V KP+G++  P       TL N +   +Y+ KD       +   + HR+DK T+GL + AKN      L     ++ V + Y  L +G       T+   I  N+ ++Q M +  + K   E +T + V+E  KD  L+E QL TG+ HQIRVHM  IG+P++GD KY  K            G  GF+ P    Y  K     N F   L+ +
  S:     9 IEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKSNYKVKLNDKI-VVTEKEVVEADIKPENLN----LDIYYEDEDVAIVYKPKGMVVHPSPGHYSGTLVNGL---MYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSKTVKRKYTALVHGNIPHDYGTIDAPIGRNKNDRQAMAVVDDGK---EAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLDIGGQALHAGIIGFEHPVTHKYIEKHATLPNDFEKLLDDI 300
>gi|171326065|ref|ZP_02914557.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70] >gi|171087952|gb|EDT34311.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70] (304 aa)
Score = 294, Expect = 7.9e-25, Identities = 75/238 (31%), Positives = 127/238 (53%)
  Q:    40 IKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQ--KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           +K+N K+ +W   LQEND LQ++L  KP    L   + E    L+V++ED++++++NK  G+   P +  +  TL N +  YL  +      +    HRLD+ T+G  + AK+      L+ +     + + Y+ L +G  K KS T+   I    ++      R ++   + +T YRV+     + ++L+E+ L TG+ HQIRVHM+ IGHP++GD  Y  +  F  Q   L + K+ F
  S:    46 VKLNGKEVSWQIPLQENDRLQLYL-YKPEASSLLPEYRE----LSVLWEDEHLLIINKDAGMDIHPSEPSQTGTLANAVAFYL--QSQGILTKVRHIHRLDRDTSGTILFAKHPLAGATLDRMLAKRQIKRTYVALVHGIMKNKSGTISAPI--GRDRHHPTRRRVSQTGAKAVTHYRVLHTFPNQQLSLVELSLDTGRTHQIRVHMSYIGHPLVGDVLYGGENTFHRQ--ALHAAKLSF 274
>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 = 294, Expect = 8.1e-25, Identities = 88/271 (32%), Positives = 148/271 (54%)
  Q:     7 KKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           +KE+E + +  F++    + + S I K I +G + VN K    +YK++END + +      + +  K++ L     L+++YED +IIV+NKP+G++  P       TL N +   LY  K+       L   + HRLDK T+G+ V AKN K    L+N     +V K Y+ +  G  K +   ++  I  +  +++ M +  + ++    +T Y+V+E+ K+  L+E  + TG+ HQIRVHMA IGHP++GD  Y  K+  F  +   L S  + F
  S:    12 EKEDEGKRIDVFLAAEL-DYTRSYIKKLIVDGLVFVNGKTVKPSYKVKENDEVVL-----NVPEAEKIDVLPEDIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNAL---LYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKIEAPIGRHPVDRKKMAVIEDGRY---ALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAYIGHPIVGDHVYGFKRQKFKLEGQALHSSVLGF 276
>gi|90022196|ref|YP_528023.1| ribosomal large subunit pseudouridine synthase D [Saccharophagus degradans 2-40] >gi|89951796|gb|ABD81811.1| ribosomal large subunit pseudouridine synthase D [Saccharophagus degradans 2-40] (321 aa)
Score = 294, Expect = 8.2e-25, Identities = 86/255 (33%), Positives = 133/255 (52%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKF--KKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           + +E     L    +  F + S S+I + IK+G + V+ K      K+   ++L +   L+   + L       +PI LN++YED++I+V+NK  GL+  P       TL N +  ++      N   A + HRLDK TTGL V AK+  T T L        VS++Y  + +G F  K K  T+   I  +  +++     EN   K  +T YRV++  +  A + +QL TG+ HQIRVHMA IG+P++GD  Y KK
  S:    11 VPQEMAGNRLDQVCADLFPDYSRSRIQQWIKSGKLLVDDKTGKAKQKVFGGENLVLEPELQEEGEWL------PEPINLNIVYEDEHILVINKQAGLVVHPAAGNWSGTLLNGLLHHV--PSLVNVPRAGIVHRLDKDTTGLMVVAKSLPTQTHLVAQLQARTVSRHYQAVVHGTFAAKDKLGTVDIAIGRHPTQRVKMAALENS-GKPAVTHYRVVKDLQGFAHVHLQLETGRTHQIRVHMAHIGYPLVGDQVYGKK 259
>gi|160901794|ref|YP_001567375.1| RluA family pseudouridine synthase [Petrotoga mobilis SJ95] >gi|160359438|gb|ABX31052.1| pseudouridine synthase, RluA family [Petrotoga mobilis SJ95] (303 aa)
Score = 293, Expect = 9.6e-25, Identities = 90/273 (32%), Positives = 148/273 (54%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWN-YKLQENDSLQIFL---RLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKFNFDKNHFLHY 287
           L  FI K++ E+ L  I   I+ G +KVN K+   N Y L+  D+++I L   +L+ + +  + + L+A+P+  ++IYEDK+++V+NKP  +   P   E++ T+   +  Y      +   E +L HRLDK T+G+ V AKN++T  EL  L  +    KYYL L  G   KKS  L   ++    +    + ++     E+             +L+EI+L TG+KHQIRV  A +G P+ GD  +  K        N+G +   L + KI F+++  H+  Y
  S:    16 LDTFIRKNYPEIKLGAIYGLIRKGFVKVNEKRVKKNNYILEIGDNVKIILDENKLEELSRPTQPS-LKARPVSFDIIYEDKDLLVINKPAKVSVHPGSKEEMATIIEGVMHY-----SRGEFEPHLVHRLDKLTSGVMVVAKNKQTARELTQLIKSRETRKYYLTLLVGNLNKKSGELVSTVYGKTAQLKFNLKKKFDLFGEL------------YSLVEIELYTGRKHQIRVQFADLGFPIAGDDNHGDKKQNKLLRKNYGLKRIFLHASKISFDYNNKHYDFY 282
>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 = 293, Expect = 9.9e-25, Identities = 87/259 (33%), Positives = 147/259 (56%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I + ++KE +N  L   +SK F++ S S +   I  G++ VN+K+   NYKL+  D+++I +   P  K L++   + K  L+VIYEDK++IVVNKP+ ++  P       TL N +  +  +    N +    + HR+DK T+G+ V AKN  +   L   +   ++S+ Y+ L  G  K +  T++  I  +   +I M + ++ +     +T Y+VI++ K+  L+E +L TG+ HQIRVHM+ I HP++GD  Y  K
  S:     4 ISLQVEKEFDNVRLDLCLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIEINI---PEPKLLQIEPEDVK--LDVIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKNEQGTIEAPIGRHPVDRIKMAVVKDGR---HAVTHYKVIKRFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYK 256
>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 = 293, Expect = 9.9e-25, Identities = 88/271 (32%), Positives = 150/271 (55%)
  Q:     7 KKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           +KE+E + +  F++    + S S I K I+ G + VN K    +YK++E+D + +      IK+  K+  +     L+++YED++IIV+NKP+G++  P       TL N +   LY  K+       L   + HRLDK T+G+ V AKN K    L+N     +V K Y+ +  G  K++   ++  I  +  +++ M + ++ ++    +T Y+V+E+ K+   +E  + TG+ HQIRVH++ IGHPV+GD  Y  KK  F  +   L S  + F
  S:    12 EKEDEGKRIDVFLASEL-DYSRSYIKKLIEEGLVLVNGKNVKPSYKVKEDDEVIV-----NIKEAEKIEVVPENIPLDILYEDEDIIVINKPQGMVVHPAPGNYSGTLVNAL---LYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIKERSVLKKYVAIVEGVIKEEEGKIEAPIGRHPVDRKRMAVVQDGRY---ALTLYKVLERFKNNTFVEATIKTGRTHQIRVHLSYIGHPVVGDPVYGYKKQKFKLEGQALHSKVLGF 276
>gi|152996325|ref|YP_001341160.1| RluA family pseudouridine synthase [Marinomonas sp. MWYL1] >gi|150837249|gb|ABR71225.1| pseudouridine synthase, RluA family [Marinomonas sp. MWYL1] (323 aa)
Score = 293, Expect = 1.0e-24, Identities = 91/287 (31%), Positives = 151/287 (52%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPI------KKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNN-LWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN------FGFQFPCL--TSYKIKFNFDKNHFLHYLNK 290
           + I      Q + +F+    K +   KI   ++ G+I+VN K+T  +Y+LQ  D     +R+ PI       K +  + L+++    ++YEDK +IV+NKP GL            +    +    EK    ++E  L HRLD+ T+GL + AK +  L EL+  L   E V K YL L YG + K+   +   +  NE +    + R +   KE +T+++++ Q +  +L+E + +TG+ HQIRVH    G+P++GD KY+   +       GF+  CL  T   I  N ++  F   L+K
  S:    17 VTIDDNNTGQRIDNFLVTFLKGVPKGKIYNLLRKGEIRVNKKRTKPDYRLQNED----VVRIAPIVIAPESDKPVLSDRLKSEIESRIVYEDKGLIVINKPSGLAVHGGSGLSFGLVEVIRQMRPLEK----FIE--LVHRLDRDTSGLIMVAKKRAVLKELHTALREKEGVQKTYLALVYGSWPKRKLQVNAPLLKNELQSGERVVRVHTDGKESLTRFKLVRQFEGYSLVECEPVTGRTHQIRVHTQYAGYPIVGDEKYSPAESLKETRALGFKRLCLHATRLDIMLNGERMLFEAPLDK 308
>gi|168186684|ref|ZP_02621319.1| pseudouridine synthase, RluA family [Clostridium botulinum C str. Eklund] >gi|169295320|gb|EDS77453.1| pseudouridine synthase, RluA family [Clostridium botulinum C str. Eklund] (323 aa)
Score = 293, Expect = 1.1e-24, Identities = 92/276 (33%), Positives = 152/276 (55%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI--FLRLKPIKKELKLNFLEAK-PILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEK------KDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKF 277
           ++I I   E  Q L  F  K  +++ L  I K+++ GDI+VN KK   NY L+E D ++       K  K  +   F E     + + YED+N++++ K  G++   DK +   TL + +  YL+ K      K+  +  A  C+RLD+ T+G+ +  KN K+L  LN +     +SKYY  L  GK K+     + +I  ++   I EI  + K N K+I  +  VI+     + LE+ L+TG+ HQ+R H++ +G+P++GD KY  +         +G  F  L +YK+ F
  S:     1 MRIEIGPNEAGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLEEEDVVETKYIESYKKNKNNVPKKFQEVNFSSIKIAYEDENMLIIEKWPGVLVHSDKKDGDPTLTDYVLSYLFNKGEYIPEKEVTFTPAP-CNRLDRNTSGMVIFGKNFKSLKLLNEMIRERKISKYYNALVKGKIKEGR--YEAYISKDQINNISEIHLDKKPNSKKIAMEVSVIDTVGTFSFLELDLITGRSHQLRAHLSFLGNPIIGDDKYGDRKLNSFFNNKYGLSFQFLYAYKLIF 290
>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 = 293, Expect = 1.2e-24, Identities = 93/286 (32%), Positives = 148/286 (51%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFPCLTSYKIKFNFDKNHFLHYLNKL 291
           I++ +  Q +   +S   K+ S S++   IK G +KVN K    NYK++ ND + +    + ++ ++K   L     L++ YED+++ VV KP+G++  P       TL N +   +Y+ KD       +   + HR+DK T+GL + AKN      L     ++ V + Y  L +G       T+   I  N+ ++Q M +  + K   E +T + V+E  KD  L+E QL TG+ HQIRVHM  IG+P++GD KY  K            G  GF+ P    Y  K     N F   L+ +
  S:     9 IEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKSNYKVKLNDKI-VVTEKEVVEADIKPENLN----LDIYYEDEDVAVVYKPKGMVVHPSPGHYSGTLVNGL---MYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSKTVKRKYTALVHGNIPHDYGTIDAPIGRNKNDRQSMAVVDDGK---EAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLDIDGQALHAGIIGFEHPVTHEYIEKHATLPNDFEKLLDDI 300
>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 = 293, Expect = 1.2e-24, Identities = 79/277 (28%), Positives = 139/277 (50%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF-GFQFPCLTSYKIKF 277
           M  + ++ +   + +  F+S+   +LS S   K ++ G + +       NYK  E D L + L        ++++ +     L+V+YED ++IV+NKP G++  P       TL N +  +  +        L   + HR+D+ T+GL +AAK+      L       ++ + Y  +  G FK+   T++  I  +  +++ M ++      +E +T Y V+E+      L+ +L TG+ HQIRVHMA IGHP+LGDT Y  K  + G    CL + ++ F
  S:     1 MTPLTLRADRVGERVDQFLSRQLPQLSRSAAQKLLEEGAVTLKGLPVKKNYKTAEGDELVLSL-----PDPVEVDVVPQDIPLDVVYEDGDVIVINKPVGMVVHPAAGHPDGTLVNALLYHCGKSLSGINGELRPGIVHRIDRDTSGLIIAAKSDFAHLALAEQLQDHSLYREYEAVAVGGFKEDEGTVRAPIARHPTDRKKMAVNFLQ--GREAVTHYTVLERFSGCTHLQCRLETGRTHQIRVHMAHIGHPLLGDTVYGSKKPYPGLAGQCLHARRLSF 274
>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 = 292, Expect = 1.5e-24, Identities = 75/226 (33%), Positives = 123/226 (54%)
  Q:    35 IKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +K G +KVN K    NY+L   DS+++ L   P  KE  +   E  P L+++YED++II++NKP+ ++  P       TL N +   +Y   D+       +   + HR+D  TTG  V  KN K    L+      ++ + Y+ + +G  K+ S T+   I  +   +  ++    K  ++ +T Y+V+E+  D   ++ +L TG+ HQIRVHMASIGHP++GD  Y  K
  S:     1 MKEGYVKVNQKPVKSNYRLSFGDSVEVTL---PEAKEPDI-VPENIP-LDILYEDQDIIMINKPKQMVVHPAPGHYSGTLVNAL---MYHCGDELSGINGCMRPGIVHRIDMDTTGSLVVCKNDKAHQSLSEQLKVHSIRRIYVAIVHGNIKEDSGTVNAPIGRHPTDR-KKMSTHCKNGRDAVTHYKVLERFGDYTYIQCELETGRTHQIRVHMASIGHPLVGDEVYGPK 222
>gi|89891672|ref|ZP_01203175.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria bacterium BBFL7] >gi|89516007|gb|EAS18671.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria bacterium BBFL7] (349 aa)
Score = 292, Expect = 1.5e-24, Identities = 74/246 (30%), Positives = 132/246 (53%)
  Q:    12 NQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI--DRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++ L +FI  + +    SKI +SIK+G ++VN +    NYK++  D +++  +  P +     N L  + I L+++YED  ++VVNKP G++  P       TL N +  +     + +     L HR+DK T+GL V AK +  ++ L+  +  +   + Y+ + +G F ++S T++  I  + + ++       E  F  K  +T + VIE    + ++  +L TG+ HQIRVHM  IGH +  D +Y
  S:    36 DKYLMNFIENATR----SKIQQSIKDGAVRVNDEVVKSNYKVKAGDHIRVLFKHPPHE-----NLLVPEDIPLDIVYEDDTLVVVNKPAGMVVHPGHGNYSGTLINALIHHFDNLPNNSSNRPGLVHRIDKDTSGLLVVAKTEHAMSYLSAQFAAKTSEREYVAIVWGNFDEQSGTVEGNIGRHPKNRLQNYVWSGEEAFKGKPAVTHWSVIEGLGYVTMISCKLETGRTHQIRVHMKHIGHTLFNDERY 276
>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 = 292, Expect = 1.6e-24, Identities = 81/259 (31%), Positives = 130/259 (50%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQ-KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQ 266
           +E  ++ L   +S+ F   S S I K   +G I VN K    +YK++  D + I      +   + ++ +     L++IYED ++I+VNKP+G++  P       TL N +  +               + HR+D  TTG+ V  KN      L+   +  ++++ Y  + YG       T+   I  + ++++ M I+  N   +  +T YRV+E+       +E QL TG+ HQIRVHMASIGHP+LGD  Y  KK  F  Q
  S:    10 EEWTDRRLDKVLSEYFDGYSRSFIKKLFDDGLILVNSKAVKPSYKVRAGDMIDI-----SVPDPVSIDIVPEDIPLDIIYEDDDVILVNKPKGMVVHPAPGHYSGTLVNGLMYHFGSSLSGINGEFRPGIVHRIDMDTTGVLVVCKNDNAHRALSEQLHEHSITRKYYAIVYGNISSDEGTVDAPIGRSPKDRKKMAINNRN--GRRAVTHYRVLERFGGRYTYIECQLETGRTHQIRVHMASIGHPILGDEVYGPKKCPFKLQ 266
>gi|118444019|ref|YP_877712.1| ribosomal large subunit pseudouridine synthase C, putative [Clostridium novyi NT] >gi|118134475|gb|ABK61519.1| ribosomal large subunit pseudouridine synthase C, putative [Clostridium novyi NT] (323 aa)
Score = 291, Expect = 1.6e-24, Identities = 92/276 (33%), Positives = 153/276 (55%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI--FLRLKPIKKELKLNFLEAK-PILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANL-------CHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK-------GNFGFQFPCLTSYKIKF 277
           ++I I   E  Q L  F  K  +++ L  I K+++ GDI+VN KK   NY L+E D ++       K  KK +   F E     + + YED+N++++ K  G++   DK +   TL + +  YL+ K +  Y+  N        C+RLD+ T+G+ +  KN K+L  LN +     +SKYY  L  GK ++     + +I  ++   I EI    K N K+I  + +VI+     + LE+ L+TG+ HQ+R H++ +G+P++GD KY  +         +G  F  L +YK+ F
  S:     1 MRIEIGPNEAGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLEEEDVVETKYIESYKKNKKNVPKKFQEVNFSSIKIAYEDENMLIIEKWPGVLVHSDKKDGDPTLTDYVLSYLFNKGE--YIPENEVTFTPAPCNRLDRNTSGMVIFGKNFKSLKLLNEMIRERKISKYYNALVKGKIREGR--YEAYISKDQINNISEIHLNKKPNSKKIAMEVKVIDTVGTFSFLELDLITGRSHQLRAHLSFLGNPIIGDDKYGDRKLNSFFNNKYGLSFQFLYAYKLIF 290
>gi|149280326|ref|ZP_01886447.1| pseudouridylate synthase, 23S RNA-specific [Pedobacter sp. BAL39] >gi|149228875|gb|EDM34273.1| pseudouridylate synthase, 23S RNA-specific [Pedobacter sp. BAL39] (343 aa)
Score = 291, Expect = 1.7e-24, Identities = 77/254 (30%), Positives = 135/254 (53%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE--KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I + K +    +  F+    +  S ++I  +I  G++ VN K    +YK++  D + I     P   E+   + E  P L+++YED +++VVNKP G++  P  N    TL N +  +  +  +   N     L HR+DK T+GL + +KN+ T+T+L   +   ++++ Y+ L +G   +   T+  FI  + + +I M++  + +  K  +T Y V+E+   + L+  QL TG+ HQIR HM  IGHP+  D  Y
  S:    21 IVVDKGQSLLRVDKFLMGRMENASRNRIQNAIDAGNVLVNGKTVKSSYKVKPADEISIVFPHPPRDTEV---YPEDIP-LDIVYEDNDLLVVNKPAGMVVHPGYNNYTGTLVNALAFHFEQLPQLPGNEGRPGLVHRIDKDTSGLLLISKNEITMTKLAKQFFDHSITRKYIALAWGDIAENG-TVTGFIGRSLKNRIVMDVYDDEEKGKWSVTHYTVLERLGYVTLISCQLETGRTHQIRAHMQHIGHPLFNDANY 272
>gi|86156486|ref|YP_463271.1| ribosomal large subunit pseudouridine synthase C [Anaeromyxobacter dehalogenans 2CP-C] >gi|85772997|gb|ABC79834.1| ribosomal large subunit pseudouridine synthase C [Anaeromyxobacter dehalogenans 2CP-C] (339 aa)
Score = 291, Expect = 2.0e-24, Identities = 77/276 (27%), Positives = 142/276 (51%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPI--KKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNT-EAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIK 276
           MIQ+ +  +   Q L   + K+ +++ LS + K  +   ++VN  +   +  + E D + I    + +  K          +    V++ED +++ V+KP GL   P    +  TL    + YL    D      + +  HRLD+ T+G+ + AK++K +  L   + T E V K YL L  GK  +++ T+   + L+E +Q  +       N +E +T+++V+   K+++LL + + TG+ HQIR H+ ++GHPV GD +Y   G+F F     T + ++
  S:     1 MIQLTVSADAAGQRLDKLVRKALRDVPLSHVYKMFRTRKVRVNGARGKADQVVAEGDVVVIRGDEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIEGATLVEMARGYLKTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLGETFTTGEGVHKTYLALVKGKMPREAGTID--LPLSEHEQTSKSKAMRGVNFQEALTRWKVVSAAKEISLLAVTIETGRTHQIRRHLEAVGHPVAGDRRY---GDFAFNRTARTRWGLR 277
>gi|168179470|ref|ZP_02614134.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC 2916] >gi|182669738|gb|EDT81714.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC 2916] (300 aa)
Score = 291, Expect = 2.1e-24, Identities = 77/254 (30%), Positives = 145/254 (57%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +KK   N  +KD++ +  + LS   I K++++G + VN +K    +KL ++D ++I++     +++   N       + ++YED +IIV+NK  G++  P K     TL+N I  +  +  +K+ +   L  RLD+ T+GL + AKNQ +   L +  + ++  K Y+ + +G  K+K   +   I+  EE + ++   + +  +E IT Y+V+E+    +++ ++L TG+ HQIRVHM+ +GHP+ GD+ Y K
  S:     9 VKKINHNIDIKDYL-REMENLSGRFIRKAVRDGRVFVNEEKVIKKHKLSQDDLIEIYM-----QEDEHQNIEPEDMNIEIVYEDNDIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVR--LVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRINLPIYKEEESESIKRIVDER-GQESITTYKVLEELSKGSVVRLELETGRTHQIRVHMSHLGHPLYGDSLYGK 253
>gi|187778438|ref|ZP_02994911.1| hypothetical protein CLOSPO_02032 [Clostridium sporogenes ATCC 15579] >gi|187772063|gb|EDU35865.1| hypothetical protein CLOSPO_02032 [Clostridium sporogenes ATCC 15579] (299 aa)
Score = 290, Expect = 2.4e-24, Identities = 83/254 (32%), Positives = 150/254 (59%)
  Q:     4 IFIKKEEENQI-LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           IF+ KE  + I +KD++ K  + LS   + K++++G I VN +K    +KL ++D ++I++      +E +   +E + I + ++YED +IIV+NK  G++  P K+    TL+N I  +  +K +K+ +   L +RLD+ T+GL + AKNQ +   L +  + ++  K Y+ + +G  K+K   +   I+  E + I  I  E    +E IT Y V+E+    ++++++L TG+ HQIRVHM+ +GH + GD+ Y
  S:     6 IFVVKEINHNIDIKDYL-KEIENLSGRFVRKAVRDGRIFVNGEKVIKKHKLSQDDLIEIYM------QEDEHQNIEPEDINIEIVYEDSDIIVINKKPGIVVHPTKSHSTGTLSNGILYHFKKKGEKSIVR--LVNRLDRDTSGLVIVAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEENESIKRIVDER--GQESITTYEVLEELSKGSVVKLELETGRTHQIRVHMSHLGHHLYGDSLY 250
>gi|168181665|ref|ZP_02616329.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf] >gi|182675008|gb|EDT86969.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf] (300 aa)
Score = 290, Expect = 2.6e-24, Identities = 77/254 (30%), Positives = 145/254 (57%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +KK   N  +KD++ +  + LS   I K++++G + VN +K    +KL ++D ++I++     +++   N       + ++YED +IIV+NK  G++  P K     TL+N I  +  +  +K+ +   L  RLD+ T+GL + AKNQ +   L +  + ++  K Y+ + +G  K+K   +   I+  EE + ++   + +  +E IT Y+V+E+    +++ ++L TG+ HQIRVHM+ +GHP+ GD+ Y K
  S:     9 VKKINHNIDIKDYL-REMESLSGRFIRKAVRDGRVFVNKEKVIKKHKLSQDDLIEIYM-----QEDEHQNIEPEDMNIEIVYEDNDIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVR--LVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRINLPIYKEEESESIKRIVDER-GQESITTYKVLEELSKGSVVRLELETGRTHQIRVHMSHLGHPLYGDSLYGK 253
>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 = 290, Expect = 2.7e-24, Identities = 80/260 (30%), Positives = 130/260 (50%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           M Q  I KE   Q +   +     + S + + + I  G + VN K+   N K+Q+ D + +    +P  +E++L  L     L+V+YED ++IVVNKPRGL+  P    +  TL N +   L+  KD       +   + HR+DK T+GL +AAK+      L      +   + Y  + +G       T+   I  + +++Q M +   N  ++  +T + + E  K  + +  +L TG+ HQIRVH   IGHP+ GD KY  K
  S:     1 MEQWIITKEHHEQRIDKVVVDLHGQASRTAVQRWINEGAVLVNEKEVKTNSKVQQGDKVTL---TEPAAQEVEL--LGEDIPLDVVYEDSDVIVVNKPRGLVVHPAPGHESGTLVNAL---LFHCKDLSGINGEIRPGIVHRIDKDTSGLIMAAKHDAAHEHLAAQLKAKTTERRYKAIVHGVIPHAKGTIDAPIGRDPKDRQKMAVTHVN--SRPAVTHFSLEETFKQYSYISCELETGRTHQIRVHFNYIGHPLAGDPKYGPK 255
>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 = 290, Expect = 2.7e-24, Identities = 71/195 (36%), Positives = 114/195 (58%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY-NKKGNFGFQFPCLTSYKIKF 277
           L+++YED++I+V+NK  G++  P K+    TL+N I  Y +E K +N +   L  RLD+ T+GL + AKNQ     L    N +   K+YL + +GK  KK  T+   I+  E+  +  +   ++  +  IT Y+V+E+ KD +L+E  L TG+ HQIRVH+  +GHP++GD+ Y N+          L +YK+ F
  S:     3 LDIVYEDEDILVINKNPGIVVHPTKSHPRGTLSNGIL-YYFEDKGENCI-VRLVSRLDRDTSGLIIIAKNQFAHMALARDMNKDTFKKFYLAIIHGKLTKKEGTIDLPIYRPEDSSLKRV--VDQKGQRSITHYKVVEEFKDASLVEFLLETGRTHQIRVHVEHLGHPIIGDSLYGNEDDTMYINRQALHAYKLVF 194
>gi|167457694|ref|ZP_02323905.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans 2CP-1] >gi|167416070|gb|EDR82789.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans 2CP-1] (339 aa)
Score = 289, Expect = 3.0e-24, Identities = 76/276 (27%), Positives = 143/276 (51%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPI--KKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNT-EAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIK 276
           MIQ+ +  +   Q L   + K+ +++ LS + K  +   ++VN ++   +  + E D + I    + +  K          +    V++ED +++ V+KP GL   P    +  TL    + YL    D      + +  HRLD+ T+G+ + AK++K +  L   + + E V K YL L  GK  +++ T+   + L+E +Q  +       N +E +T+++V+   K+++LL + + TG+ HQIR H+ ++GHPV GD +Y   G+F F     T + ++
  S:     1 MIQLTVTADAAGQRLDKLVRKALRDVPLSHVYKMFRTRKVRVNGQRGKADQLVAEGDVVVIRGDEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIEGATLVEMARGYLKTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLTETFTSGEGVHKTYLALVKGKMPREAGTID--LPLSEHEQTSKSKAMRGVNFQEALTRWKVVSAAKEISLLAVTIETGRTHQIRRHLEAVGHPVAGDRRY---GDFAFNRTARTRWGLR 277
>gi|159029548|emb|CAO87700.1| rluD [Microcystis aeruginosa PCC 7806] (308 aa)
Score = 289, Expect = 3.1e-24, Identities = 84/275 (30%), Positives = 147/275 (53%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKK-TTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP--CLTSYKI 275
           M Q+ ++   + + L  ++     +LS S++ K I+ G I++N +  T  N K+ + D L+I +   P  + L+L+   A+ I L+++YED+ +I++NKP  L+  P    +  TL N +  +         ++   + HRLDK TTG  V AK  +    L     T+   + Y+ L +G  K ++ T+   I  +  ++Q M I    K  +  +T ++V E+  +  L+E +L TG+ HQIRVH + IGHP+LGD  Y+   + G   P   L +Y++
  S:     1 MNQLNLEVAGKKERLDAWMGSQLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQGDRLKITI---PDSQPLQLS---AEAIDLDILYEDEYLIIINKPADLVVHPAPGHESGTLVNALLHHCPNLAGIGGIQRPGIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYMALVHGVPKSETGTIDLPISRHRSDRQKMAIIAVEKGGRNAVTHWQVKERLGNYTLMEFRLETGRTHQIRVHSSHIGHPILGDPLYSSGRSIGINLPGQLLHAYRL 275
>gi|153940669|ref|YP_001392256.1| RluA family pseudouridine synthase [Clostridium botulinum F str. Langeland] >gi|152936565|gb|ABS42063.1| pseudouridine synthase, RluA family [Clostridium botulinum F str. Langeland] (300 aa)
Score = 289, Expect = 3.3e-24, Identities = 77/254 (30%), Positives = 144/254 (56%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +KK   N  +KD++ +  + LS   I K++++G + VN +K    +KL ++D ++I++     +++   N       + ++YED +IIV+NK  G++  P K     TL+N I  +  +  +K+ +   L  RLD+ T+GL + AKNQ +   L +  + ++  K Y+ + +G  K+K   +   I+  EE + ++   + +  +E IT Y V+E+    +++ ++L TG+ HQIRVHM+ +GHP+ GD+ Y K
  S:     9 VKKINHNIDIKDYL-REMENLSGRFIRKAVRDGRVFVNKEKVIKKHKLSQDDLIEIYM-----QEDEHQNIEPEDMNIEIVYEDNDIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVR--LVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYNEEESESIKRIVDER-GQESITTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHPLYGDSLYGK 253
>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 = 289, Expect = 3.3e-24, Identities = 72/255 (28%), Positives = 134/255 (52%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +I + K +E   +  F+      ++ +K   +I+ G +KVN ++   NYK++  D + I L   P + E+     E  PI N++YED +++VV+K  G++  P  N    TL N +  +     +       L HR+DK T+GL V AK++  L  L   +    + + Y  L +G+ K+++ T+   +  + +++++     E  F +  +T Y+V++  + ++L++  L TG+ HQIR HM  +GHP+  D  Y
  S:    39 RIVVDKGQEPVRIDKFLMDRVPNITRNKTQNAIREGFVKVNDQEVKPNYKVRPEDIIIISLPEPPRESEV---VPEDIPI-NIVYEDDDLLVVHKEAGMVVHPAYNNWTGTLVNALAYHFKNLPENRDGRPGLVHRIDKDTSGLLVVAKSEHALQHLAKQFFDHTIERTYYALVWGEPKQEAGTIDVNLGRSLKDRRVTAAFPEGDFGRHAVTHYKVLKNLRYVSLVQCNLETGRTHQIRAHMKHLGHPLFNDATY 290
>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 = 289, Expect = 3.3e-24, Identities = 92/289 (31%), Positives = 145/289 (50%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI--------LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDREN--------KFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG-------------NFGFQFPCLTSYKIKFNFD-KNHFLHYLNKL 291
           +  +++E   Q +  F+S     LS S +   +  G ++ N K    + KL+  D++              L   +AKPI        L ++YED +++VVNKP+G++  P       TL N +   L+  K         +   + HR+DK T+GL V AK+  T   L+      +V + Y  + YG F +      D  F+       +IDR+            K   T Y+V+E+  +  LLE +L TG+ HQIRVHMASI HPV GD  Y                   GF  P +T  +++F+ +  ++F H+L  L
  S:     5 EFIVEQETAGQRIDRFLSGEDTGLSRSALQALVAEGHVQCNGKAVAKSLKLKAGDTVL-------------LEIPDAKPIEAVPQDIPLEIVYEDAHLLVVNKPKGMVVHPAPGNPDGTLVNAL---LWHCKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYQTVVYGGFAQ------DEGFVEANLGRSKIDRKKMAVYPATEPHTKYAYTGYKVLERLGEFTLLECRLKTGRTHQIRVHMASIHHPVAGDPVYGPHNCITSLHGQCLHAKTLGFVHP-ITGEQLRFDSELPDYFTHFLATL 305
>gi|188994625|ref|YP_001928877.1| ribosomal large subunit pseudouridine synthase [Porphyromonas gingivalis ATCC 33277] >gi|188594305|dbj|BAG33280.1| ribosomal large subunit pseudouridine synthase [Porphyromonas gingivalis ATCC 33277] (365 aa)
Score = 289, Expect = 3.4e-24, Identities = 74/243 (30%), Positives = 130/243 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANL--CHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF--LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +  F+       + S+I ++ + G I VN +    NY+++  D + + L L+P ++EL++   E  P L+++YED  ++V+NKP GL+  P       TL N +  YL E  + + ++ +L   HR+DK T+GL V AK  +  ++L   +  +   + Y  L +G+F     T+   I   L +  Q+     +    K  +T Y+V+E+   ++ +E +L TG+ HQIR HM  IGH +  D +Y
  S:    46 IDKFLVDRMNNATRSRIQQAAEAGAIFVNGRPVKSNYRIKPGDVVTLEL-LRP-RRELEI-IPEDIP-LDIVYEDDVLLVINKPAGLVVHPGHGNYTGTLVNALAYYLREDPEYDPMDPSLGLVHRIDKDTSGLLVVAKRAEAKSDLCKQFYYKTTHRSYRALVWGRFDYPIGTITGNIGRDLKDRLQMAVFPPDGDIGKPAVTHYQVLEELAYVSWIECRLETGRTHQIRAHMKHIGHTLFADERY 288
>gi|58337436|ref|YP_194021.1| pseudouridine synthase [Lactobacillus acidophilus NCFM] >gi|58254753|gb|AAV42990.1| pseudouridine synthase [Lactobacillus acidophilus NCFM] (302 aa)
Score = 289, Expect = 3.4e-24, Identities = 85/260 (32%), Positives = 137/260 (52%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFL-RLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK----KGNFGFQFPCLTSYK 274
           L  FIS+   +LS +++ + I++ +I VN K    +YK+Q+ D ++I +  +KP      L+ +     L+++YED ++IVVNKP+G++  P       TL N +   LY  +D           + HR+DK T+GL + AKN      L      +   + Y  + +G F ++  ++   I  N   +      EN   K+ IT ++V++Q K  +L+E QL TG+ HQIRVH+  IGH V GD  Y      KGN  F    +  +K
  S:    16 LDKFISEQLSDLSRTRVKELIQDQNILVNEKVEKVSYKIQDGDKIEITVPAVKP------LDIVAENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNAL---LYHTQDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNATARESLEQQLANKTNKRIYWAIVHGNFSEEQGSIDAPIGRNPYDRKKMAVVEN--GKKAITHFKVLKQFKGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGNGQFLHAKILGFK 273
>gi|52079396|ref|YP_078187.1| putative pseudouridine synthase YhcT [Bacillus licheniformis ATCC 14580] >gi|52784756|ref|YP_090585.1| YhcT [Bacillus licheniformis ATCC 14580] >gi|52002607|gb|AAU22549.1| putative Pseudouridine synthase YhcT [Bacillus licheniformis ATCC 14580] >gi|52347258|gb|AAU39892.1| YhcT [Bacillus licheniformis DSM 13] (305 aa)
Score = 289, Expect = 3.5e-24, Identities = 76/232 (32%), Positives = 126/232 (54%)
  Q:    35 IKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKY--RVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY-NKKGNFGFQ 266
           I N  +KVNHK    N +L+  DS+ I LR     +E +   +     L V++ED ++++VNKP G+   P++  +  TL+N +  Y     ++   +    HRLDK T+G  V AK++     L+     + +++ Y+ +  GKF+KK+ T+   I  ++   +    R +   +  +T +  +  + + D+ L  +QL TG+ HQIRVH+ASIGHP+ GDT Y   KG F  Q
  S:    40 IANEKVKVNHKSVNHNVRLESGDSVMIDLR-----EEEESGIVPEYGELPVLFEDDHMLIVNKPAGMATHPNEAGQTGTLSNLVAFYFQMNGEER--KVRHVHRLDKDTSGAVVFAKHRLAHALLDEQLQRKELARTYVAVAEGKFRKKTGTISAPIGRDKHHPVRR--RVSHSGQPAVTHFESKGYDSRHDVTLCRLQLETGRTHQIRVHLASIGHPLSGDTLYGGSKGLFQRQ 265
>gi|148358865|ref|YP_001250072.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella pneumophila str. Corby] >gi|148280638|gb|ABQ54726.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella pneumophila str. Corby] (321 aa)
Score = 288, Expect = 3.9e-24, Identities = 83/261 (31%), Positives = 123/261 (47%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           Q+ + +E  NQ +   +++   E S S I   IK G + +N+       K    D + I +    +  +  L   E  PI  +IYED  +IVVNKP GL+  P    K  TL N +  +  E +      A + HRLDK TTGL + AKN  + T L        + ++YL L +G           F    + +  M +     F ++ +T Y + +  KD  LL + L+TG+ HQIRVHM  I HPV+GD  Y  +  F
  S:     8 QLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLITINVNHTIVNTDFNLCKPENIPI-QIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQ--LLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHPKNRLKMAV---TDFGRQAVTHYNINKHYKDFTLLNVSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKF 262
>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 = 288, Expect = 4.1e-24, Identities = 83/241 (34%), Positives = 126/241 (52%)
  Q:    19 ISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           I++ F++ S ++I K +K G I VN + T   + +  ++ ++I + L P  +     ++     L +I+ED +IIV++KP  +I  P       T++N +   L+  KD++ L  A + HRLDK T+GL VAAK+      L        VS+ YL +  G+  K+    +        +  M I   N   KE IT Y  IE      L+E QL TG+ HQIRVHM SI HP++GD  YNK
  S:    14 INEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNE-----WIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNTL---LHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGTINQPIGRDPTNRTKMAI---NYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNK 244
>gi|54297242|ref|YP_123611.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate synthase) (Uracil hydrolyase) [Legionella pneumophila str. Paris] >gi|53751027|emb|CAH12438.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate synthase) (Uracil hydrolyase) [Legionella pneumophila str. Paris] (321 aa)
Score = 288, Expect = 4.1e-24, Identities = 83/261 (31%), Positives = 123/261 (47%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           Q+ + +E  NQ +   +++   E S S I   IK G + +N+       K    D + I +    +  +  L   E  PI  +IYED  +IVVNKP GL+  P    K  TL N +  +  E +      A + HRLDK TTGL + AKN  + T L        + ++YL L +G           F    + +  M +     F ++ +T Y + +  KD  LL + L+TG+ HQIRVHM  I HPV+GD  Y  +  F
  S:     8 QLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLITINVDHTIVNTDFNLCKPENIPI-QIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQ--LLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHPKNRLKMAV---TDFGRQAVTHYNINKHYKDFTLLNVSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKF 262
>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 = 288, Expect = 4.4e-24, Identities = 88/246 (35%), Positives = 139/246 (56%)
  Q:    12 NQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEA----NLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           N  L   I+ + +ELS ++I + I  G + VN K    +YK + ND ++I      I+    L  +EA+ I LNV+YEDK++IV++KP G+I  P       TL N +   L+  KD + +       + HR+DK T+GL + AKN      L+      +V++ Y+ L +G        +   I  N  ++Q M + + N  +K  IT + V+++ K+M+L+E +L TG+ HQIRVHM+ IG+PV GD KY
  S:    13 NYRLDKIIALNMEELSRTQIQEMIGRGLVLVNGKVEKASYKTKLNDQIEI-----TIEDNSDLE-IEAEDIPLNVVYEDKDVIVIDKPTGMIVHPSPGITSGTLVNAL---LFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDIAHRFLSEQLKDHSVTRRYVALVHGLIPHVQGKIDAPIGRNPNDRQSMCVTKNN--SKNAITNFTVLKRYKNMSLIECRLETGRTHQIRVHMSYIGYPVYGDPKY 253
>gi|62260278|gb|AAX77894.1| unknown protein [synthetic construct] (367 aa)
Score = 288, Expect = 4.4e-24, Identities = 83/241 (34%), Positives = 126/241 (52%)
  Q:    19 ISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           I++ F++ S ++I K +K G I VN + T   + +  ++ ++I + L P  +     ++     L +I+ED +IIV++KP  +I  P       T++N +   L+  KD++ L  A + HRLDK T+GL VAAK+      L        VS+ YL +  G+  K+    +        +  M I   N   KE IT Y  IE      L+E QL TG+ HQIRVHM SI HP++GD  YNK
  S:    55 INEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNE-----WIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNAL---LHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGTINQPIGRDPTNRTKMAI---NYRGKEAITHYTSIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNK 285
>gi|167217842|ref|ZP_02287478.1| ribosomal large subunit pseudouridine synthase, RluD subfamily protein [Listeria monocytogenes FSL J1-175] (294 aa)
Score = 288, Expect = 4.6e-24, Identities = 88/284 (30%), Positives = 141/284 (49%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD--------KNHFLHYLNKL 291
           +E  ++++ + + KS      S I   +KNGDI VN +    NYK+Q  D +        +++  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + V+E+     L+  +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+          K HFL  L KL
  S:    14 RERVDKVIAEMMGKS-----RSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY-----EVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQFLHAAKLGFDHPTTKERMMLKRHFLVPLKKL 294
>gi|194334247|ref|YP_002016107.1| pseudouridine synthase, RluA family [Prosthecochloris aestuarii DSM 271] >gi|194312065|gb|ACF46460.1| pseudouridine synthase, RluA family [Prosthecochloris aestuarii DSM 271] (347 aa)
Score = 288, Expect = 4.6e-24, Identities = 77/240 (32%), Positives = 128/240 (53%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKK---DKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI--FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++++  +  + +K+ ++I    + VN K    NY+++  DS+++   L+P   EL     E  PI ++IYED++++VVNK   ++  P       TL N I  ++ ++    D + +   + HRLDK T+GL + AKN   L  L   +    V K Y  + +G  +  +  +K  I   +   K +     E K  K  IT+YRV +     +L+E+ L TG+ HQIRVHM  +GHP+LGD  Y
  S:    39 YLAQQVENATRNKVQEAIAEHRVLVNGKTIKSNYRIKSLDSIEVTF-LRPPAPELAP---EDIPI-DIIYEDEDLMVVNKASDMVVHPAFGNWTGTLANAILHHIGKEAGDLDCSDMRPGIVHRLDKNTSGLIIIAKNSTALHRLARQFANRQVEKKYQAIVWGVPEPATGLIKTNIGRSVRNRKVMTSYPFEGKDGKTAITEYRVQQSLCYFSLVEVTLHTGRTHQIRVHMQHLGHPILGDETY 278
>gi|163765192|ref|ZP_02172225.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K] >gi|196170331|gb|ACG71304.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K] (339 aa)
Score = 287, Expect = 4.9e-24, Identities = 76/276 (27%), Positives = 142/276 (51%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPI--KKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNT-EAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIK 276
           MIQ+ +  +   Q L   + K+ +++ LS + K  +   ++VN ++   +  + E D + I    + +  K          +    V++ED +++ V+KP GL   P    +  TL    + YL    D      + +  HRLD+ T+G+ + AK++K +  L   + + E V K YL L  GK  +++ T+   + L+E +Q          N +E +T+++V+   K+++LL + + TG+ HQIR H+ ++GHPV GD +Y   G+F F     T + ++
  S:     1 MIQLTVTADAAGQRLDKLVRKALRDVPLSHVYKMFRTRKVRVNGQRGKADQLVAEGDVVVIRGDEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIEGATLVEMARGYLRTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLTETFTSGEGVHKTYLALVKGKMPREAGTID--LPLSEHEQTSRSKALRGVNFQEALTRWKVVSAAKEISLLAVTIETGRTHQIRRHLEAVGHPVAGDRRY---GDFAFNRTARTRWGLR 277
>gi|150020811|ref|YP_001306165.1| RluA family pseudouridine synthase [Thermosipho melanesiensis BI429] >gi|149793332|gb|ABR30780.1| pseudouridine synthase, RluA family [Thermosipho melanesiensis BI429] (293 aa)
Score = 287, Expect = 4.9e-24, Identities = 84/246 (34%), Positives = 134/246 (54%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           L  F+ K  + + LS I K I+ G + VN K+    +++L+  D ++I        +E     +  K    ++YED+N++++NKP G+   P K   I TL   I+  +Y  K+ N+    L HRLDK+T+G+ V AKN  T  ELN + ++ AV K Y  LC G+  KKS+ +K  I L+ +  +   +++ +F   +             +LL +Q+ TG+KHQIR H++ IGHPV+GD  Y  K
  S:    12 LDKFLRKQLQNMPLSAIYKIIRKGKVLVNGKRVKEPSFRLEIGDEIEIKEETTKYNREKNNQIIPIKMDFEILYEDENLLIINKPAGIPIHPGKGTHIATL---IEGLMYYGKEHNF-TPYLVHRLDKHTSGVFVVAKNVNTARELNEIISSRAVEKVYTTLCVGEM-KKSEVIK--IPLDGKNAVTIYEKQKQFKSGL----------GYFSLLRVQIKTGRKHQIRKHLSLIGHPVIGDDLYGDK 241
>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 = 287, Expect = 5.0e-24, Identities = 84/252 (33%), Positives = 137/252 (54%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLR-LKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++E   L   I++   +LS +KI + + + +I VN+K    +YK+Q  D + + +  +KP+        LEA+ + L+++YED ++IVVNKP+G++  P       TL N +   LY  +D           + HR+DK T+GL + AKN K    L      +   + YL + +G F+ K+  +   I  N   ++ M +   N   K  +T + V+EQ K+ +L++  L TG+ HQIRVHM  IGHP+ GD  Y  K
  S:    10 DDEKGRLDKVIAEKITDLSRTKIKELVNDKNILVNNKAEKVSYKVQSGDVIDVTIPPVKPLS-------LEAENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVNGL---LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDKARESLEKQLAEKINKREYLAIVHGNFEVKNGVINAPIGRNPNNRKQMAV---NPKGKAAVTHFTVLEQFKNYSLVKCVLETGRTHQIRVHMKYIGHPLAGDPLYGPK 255
>gi|124516586|gb|EAY58094.1| Pseudouridylate synthase, 23S RNA-specific [Leptospirillum sp. Group II UBA] (339 aa)
Score = 287, Expect = 5.0e-24, Identities = 82/275 (29%), Positives = 147/275 (53%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKP---ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNY-------------LEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQ-KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP--CLTSYKIKF 277
           +  + + E+ + L  ++SK+    + S++ + ++   + +N      ++K++  D +++ +   P + +       A+P    L ++YED+++IV++KP GL+  P       TL N +  +   + D+               L A L HRLD+ T+G+ V  K +  + +L N +   +VSK YL L  G   KK   +   I  +   +     R++   K  +T+YRV+E   ++ +LLE+ LLTG+ HQIRVH   +G P+LGD  Y  KG     FP   L ++K+ F
  S:    20 EFLVPRGEQPKRLDIYLSKNCLGFTRSRVQRLLEEKLVTINDIYPASSHKVRGGDRIRVLI--PPPRSQ------TAQPENIRLEILYEDEDLIVISKPPGLVVHPAPGHSSGTLVNGLLFHFQSQGDEQKKGEPEEEEEAERPLRAGLVHRLDQDTSGVMVVGKTESVVLDLMNQFKDRSVSKKYLALVKGILPKKRGEINAPIGRSTHDRKKFTVRQD--GKPSVTRYRVLETYHENYSLLEVTLLTGRTHQIRVHFRYLGFPLLGDAVYGSKGTENKNFPRQMLHAWKLSF 303
>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 = 287, Expect = 5.2e-24, Identities = 83/241 (34%), Positives = 126/241 (52%)
  Q:    19 ISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           I++ F++ S ++I K +K G I VN + T   + +  ++ ++I + L P  +     ++     L +I+ED +IIV++KP  +I  P       T++N +   L+  KD++ L  A + HRLDK T+GL VAAK+      L        VS+ YL +  G+  K+    +        +  M I   N   KE IT Y  IE      L+E QL TG+ HQIRVHM SI HP++GD  YNK
  S:    29 INEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNE-----WIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNAL---LHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGTINQPIGRDPTNRTKMAI---NYRGKEAITHYTSIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNK 259
>gi|148380931|ref|YP_001255472.1| pseudouridine synthase, RluA family [Clostridium botulinum A str. ATCC 3502] >gi|153932924|ref|YP_001385300.1| RluA family pseudouridine synthase [Clostridium botulinum A str. ATCC 19397] >gi|153936215|ref|YP_001388708.1| RluA family pseudouridine synthase [Clostridium botulinum A str. Hall] >gi|148290415|emb|CAL84542.1| putative ribosomal large subunit pseudouridine synthase [Clostridium botulinum A str. ATCC 3502] >gi|152928968|gb|ABS34468.1| pseudouridine synthase, RluA family [Clostridium botulinum A str. ATCC 19397] >gi|152932129|gb|ABS37628.1| pseudouridine synthase, RluA family [Clostridium botulinum A str. Hall] (300 aa)
Score = 287, Expect = 5.3e-24, Identities = 77/254 (30%), Positives = 143/254 (56%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +KK   N  +KD++ +  + LS   I K++++G + VN +K    +KL ++D ++I++     +++   N       + ++YED +IIV+NK  G++  P K     TL+N I  +  +  +K+ +   L  RLD+ T+GL + AKNQ +   L +  + +   K Y+ + +G  K+K   +   I+  EE + ++   + +  +E IT Y V+E+    +++ ++L TG+ HQIRVHM+ +GHP+ GD+ Y K
  S:     9 VKKINHNIDIKDYL-REMENLSGRFIRKAVRDGRVFVNKEKVIKKHKLSQDDLIEIYM-----QEDEHQNIEPEDMNIEIVYEDNDIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVR--LVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDRFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDER-GQESITTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHPLYGDSLYGK 253
>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 = 287, Expect = 5.3e-24, Identities = 80/258 (31%), Positives = 126/258 (48%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN------KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN 282
           ELS S+ ++ IK G + VN +     Y +QE D +        I KE  L++      L++IY+D ++ VVNKP+G++  P       TL N +  ++ +    N  +   + HR+DK T+GL + AKN +    L      +   + YL + +G        +        E  I   D++ K        K  IT++ V+E+  D  L+E+ L TG+ HQIRVHMA IGHP+ GD  Y  +   G +   L +  + F    N
  S:    21 ELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITF-----DIPKEEVLDYQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVI--------EAPIGRSDKDRKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHPLAGDPVYGPRKTLGGKGQFLHAQTLGFTHPSN 272
>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 = 287, Expect = 5.5e-24, Identities = 80/258 (31%), Positives = 126/258 (48%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN------KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN 282
           ELS S+ ++ IK G + VN +     Y +QE D +        I KE  L++      L++IY+D ++ VVNKP+G++  P       TL N +  ++ +    N  +   + HR+DK T+GL + AKN +    L      +   + YL + +G        +        E  I   D++ K        K  IT++ V+E+  D  L+E+ L TG+ HQIRVHMA IGHP+ GD  Y  +   G +   L +  + F    N
  S:    21 ELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITF-----DIPKEEVLDYQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVI--------EAPIGRSDKDRKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHPLAGDPVYGPRKTLGGKGQFLHAQTLGFTHPSN 272
>gi|150010359|ref|YP_001305102.1| RNA pseudouridylate synthase [Parabacteroides distasonis ATCC 8503] >gi|149938783|gb|ABR45480.1| RNA pseudouridylate synthase [Parabacteroides distasonis ATCC 8503] (304 aa)
Score = 287, Expect = 5.8e-24, Identities = 79/252 (31%), Positives = 135/252 (53%)
  Q:    11 ENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKT-TWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN 262
           E+  L  F+ +  KE S S +   +  G I VN K T  ++  L  ND++ I       + +++ N     P+L +++ED ++IV+NK  GL+       K  T    +  YL E   +N +   + HRLD+ T+G+ + AKNQK   +L + W+     + Y+ +  G+ +K +D +   +  N+  Q+     ++   KE IT+YR+++     +L+E+ L TG+K+QIR  M SIGHP+ GD+KY  + N
  S:    26 ESNTLLPFLFELLKEQSRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYG----RGKVEFN----NPLLRIVWEDDDLIVINKREGLLSVSTDRIKERTAYRILSDYLKECDPRNKI--FVLHRLDRDTSGIMMFAKNQKVKEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHMQVYVT--QDGDGKEAITRYRLLQTNNRYSLVELDLETGRKNQIRAQMQSIGHPIAGDSKYGAETN 266
>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 = 287, Expect = 6.1e-24, Identities = 94/292 (32%), Positives = 152/292 (52%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG--------------NFGFQFPCLTSYKIKFNFD-KNHFLHYLNKLN 292
           M + F  + EE   +  ++++   E S S + K IK   IKVN+K    NY+L   D +++ +   P  KE  +   E + I L+++YED+++IVVNKP+ ++  P       TL N +  +   +           + HR+D  TTG  +  KN      L       ++++ Y  + +G  K++  T+   I  +  +++ M I  +N  N   IT Y+V+++  D   ++ +L TG+ HQIRVHMASIGHP+LGD  Y  K                 GF  P    Y I+ N    ++FL+ L KLN
  S:     1 MTEYFTVENEEGDRIDRYLAEEMPERSRSYLQKLIKEQYIKVNNKPVKANYRLVLGDRVEVCI---PEAKEPDI---EPENIPLDILYEDEDVIVVNKPKQMVVHPAPGHYSGTLVNALMYHCGNELSGINGTSRPGIVHRIDMDTTGSLIICKNDMAHQSLAVQLEEHSINRIYEAIVHGNIKEEEGTVNAPIGRHPTDRKKMSIHAKNARNA--ITHYKVLKRFGDYTYIQCKLETGRTHQIRVHMASIGHPLLGDQVYGPKKCPFSKLVGQTLHARTLGFIHPRTNEY-IEVNAPLPDYFLNLLEKLN 302
>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 = 286, Expect = 6.2e-24, Identities = 87/254 (34%), Positives = 145/254 (57%)
  Q:     6 IKKEEENQILKDFISKSFK-ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN---LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMA-LLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +++E+E + L  +I++    E+S + I  +I  G I VN  +   +YK+++ D +QI    + +++  + N L     LN++YED+ +IV+NKP GLI  P  + K  TL N +  ++ +  DK   + N   + HRLDK T+G+ V AKN  +   L+  +      KYYL +  G  K+K   +   +       I+   R   +N KE IT+Y+ +++  D+A L+ I+L TG+ HQIRVH   IG+P++GD+ Y K
  S:     8 VEREDEQKRLDIYIAQKMPIEISRNLIQNAITKGQITVNGSQKKPHYKVKQGDEIQIDFH-ELVEETKEENILPENIPLNILYEDEELIVINKPAGLIVHPTPSIKTGTLVNALMHHV-KDLDKTMQDPNRLGIVHRLDKETSGVLVVAKNAFSHHLLSKEFKERKTMKYYLAIVEGTLKEKEGEINLPL---GRHPILRHKRAVVYNGKEAITEYKTLKEFGDLATLVWIRLRTGRTHQIRVHFKYIGNPLIGDSLYGK 262
>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 = 286, Expect = 6.5e-24, Identities = 78/243 (32%), Positives = 129/243 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL--YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN---EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +  F+       S +KI  +I N  I VN   T  NYK++  D +QI L   P   EL     E  P L+++YED+ ++VV+KP G++  P  N    TL N +  Y         N     L HR+DK T+GL V AK + +L  L   +   ++++ Y  L +G+ + ++ T+   I L+   ++++I+      +  K  +T Y+V+E+ + ++L++  L TG+ HQIR HM  +GHP+  D  Y
  S:    30 IDKFLIDRLPNTSRNKIQLAIDNQFILVNGIPTKANYKIRPYDKIQIVLPNPPRNNEL---IPENIP-LDIVYEDEALMVVHKPAGMVVHPGYNNWTGTLVNALIYYFDNLPTAPNNIGRPGLVHRIDKDTSGLLVVAKTEASLIALAKQFYDHSIARTYYALIWGEPETETGTID--INLDRSLQDRRIVAPYTNPEKGKRAVTHYQVVERLRYVSLVKCTLETGRTHQIRAHMKHMGHPIFADAAY 271
>gi|86132824|ref|ZP_01051415.1| ribosomal large subunit pseudouridine synthase D [Cellulophaga sp. MED134] >gi|85816530|gb|EAQ37717.1| ribosomal large subunit pseudouridine synthase D [Dokdonia donghaensis MED134] (347 aa)
Score = 286, Expect = 6.5e-24, Identities = 81/267 (30%), Positives = 135/267 (50%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI---DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYK 274
           K +E   +  F+    +  + +KI K+ KNG I+VN+K    NYK++  D ++      P   E  L   E  P L++IYED +++VVNKP G++  P       TL N +  ++    + +     L HR+DK T+GL V AK +  +T L+  +  +   + Y+ + +G       T++  I  + + ++      D E +  K  +T Y+V+E+   +  +  +L TG+ HQIRVHM  IGH +  D +Y   GN   +    T YK
  S:    26 KGQEPLRVDKFLMNFVENATRNKIQKAAKNGSIQVNNKVVKQNYKVKAGDVVRAMFEHPP--HEFLLT-PEDIP-LDIIYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALIHHIDNLPNNSSERPGLVHRIDKDTSGLLVVAKTEHAMTHLSKQFFNKTTEREYVAIVWGNVVDDEGTIEGNIGRHPKNRLQNTVFKDDEEEQGKPAVTHYKVLERLGYVTQVACKLETGRTHQIRVHMKYIGHTLFNDERYG--GNAILKGTSFTKYK 289
>gi|83857910|ref|ZP_00951437.1| ribosomal large subunit pseudouridine synthase D [Croceibacter atlanticus HTCC2559] >gi|83848090|gb|EAP85960.1| ribosomal large subunit pseudouridine synthase D [Croceibacter atlanticus HTCC2559] (356 aa)
Score = 286, Expect = 6.7e-24, Identities = 77/250 (30%), Positives = 131/250 (52%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-----MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           K +E   +  F+    +  + +KI K+ K G+I VN      NYK++  D +++     P +  L     E  P LN+++ED +++VVNKP G++  P       TL N +  +     + +     L HR+DK T+GL V AK +  +T L+  +  +  S+ Y+ L +G  +    T++  I  + + ++     +E D + K  K  +T Y+VIE+   + LL  +L TG+ HQIRVH+  IGH +  D +Y
  S:    35 KGQEPLRVDKFLMNFIENATRNKIQKAAKEGNIYVNDAVVKQNYKVKAGDEVKVLFEHPPYEMLLTP---EDIP-LNIVHEDDDVLVVNKPAGMVVHPGHGNYSGTLINALVFHFDNLPNNSSNRPGLVHRIDKDTSGLLVVAKTEHAMTHLSKQFFNKTSSREYIALVWGNVEDDQGTIEGHIGRHPKNRLQNTVFLEDDADEK-GKPAVTHYKVIERLGYVTLLSCKLETGRTHQIRVHLKHIGHTLFNDERY 284
>gi|153953520|ref|YP_001394285.1| RluD1 [Clostridium kluyveri DSM 555] >gi|146346401|gb|EDK32937.1| RluD1 [Clostridium kluyveri DSM 555] (299 aa)
Score = 286, Expect = 6.8e-24, Identities = 91/272 (33%), Positives = 149/272 (54%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG-NFGFQFPCLTSYKIKF 277
           +K++E+   LK+++ K  +  S   I  +  +G I++++K+   N+ L+  D +   L    IK+E + N    K  + V+YED++IIVVNK  G++  P ++    TL N +  Y ++K  +N +   L  RLD  T+GL + AKNQ     L+    +E   K Y+ + +GK K+    +   I+  E   I  I   +K  +  IT Y+VIE+ K   LL++ L TG+ HQIRVH++ +GHP+ GDT Y  +G N       L +Y++KF
  S:    10 VKEQEQGLKLKEYLKK-IQRFSGRLIRGAALSGRIEIDNKRVKLNHVLKSGDVICFNL----IKEESQ-NIGAEKMDIEVVYEDRDIIVVNKKPGIVVHPTRSYPSGTLANGLI-YYFQKSGENCI-VRLVSRLDMDTSGLIIVAKNQFAHMCLSRDMKSEDFEKSYIAVIHGKMKEGQGIIDLPIYRPEGDDIRRI--VDKRGQRSITHYKVIEEFKHDQLLKLILKTGRTHQIRVHLSYLGHPLYGDTLYGIEGDNRYINRQALHAYRLKF 272
>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 = 286, Expect = 7.9e-24, Identities = 83/255 (32%), Positives = 127/255 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN------KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I KE  N++ K        ELS S+ +++IK G + VN K     Y ++E D +   L      +E  L +      L++IYED ++ VVNKP+G++  P       TL N +   +Y  KD       +   + HR+DK T+GL + AKN K    L      +   + Y+ + +G        +        E  I   D++ K        K  +T++ V+E+  +  L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:     4 IIKEAGNRLDKSL--ADLTELSRSQANEAIKAGTVLVNGKSAKAKYVVKEGDVITYVL-----PEEEVLEYKAEDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNAL---MYHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVI--------EAPIGRSDKDRKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR 250
>gi|169335579|ref|ZP_02862772.1| hypothetical protein ANASTE_01994 [Anaerofustis stercorihominis DSM 17244] >gi|169258317|gb|EDS72283.1| hypothetical protein ANASTE_01994 [Anaerofustis stercorihominis DSM 17244] (307 aa)
Score = 285, Expect = 8.4e-24, Identities = 95/283 (33%), Positives = 155/283 (54%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK------KGNFGFQFPCLTSYKIKFNFDKNH 283
           M +I I +E  +  L  FISK    LS  +I K ++   IKVN KK   +Y+ ++ D +Q FL  +  K++   + L     LN+IYEDKNII+++KP G++ Q D + K D ++N I  YL  K         +  RLD  T+G+ +A KN++ L  LN +   + + K YL L  G F ++       I  N+E +++  +++   + E+  ++ + ++ K   LLE++L+TGK HQIR  +  +G PV+GD KYNK      K +F      L  YK+   + + +
  S:     1 MREIIITEEFMDMRLDRFISK-VTTLSKGEIQKLLRKKYIKVNGKKQEGSYRTEKLDKVQFFLSDEVFKQDNLHSKLNTNN-LNIIYEDKNIILIDKPSGILSQADGSSKEDIVSNLIS-YLNSK------STGIVTRLDLNTSGIVLAGKNRRALMLLNEMSKNKLIDKRYLTLVRGDFDREGKVTHYGIKDNKENKLILGNKKVDGSFEVSAEFIIKKRYKYHTLLEVRLITGKTHQIRSQLDKMGFPVVGDRKYNKSKQCGNKDDFKINRQFLHCYKLTLKYSEKY 280
>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 = 285, Expect = 8.5e-24, Identities = 82/241 (34%), Positives = 126/241 (52%)
  Q:    19 ISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           I++ F++ S ++I K +K G I VN + T   + +  ++ ++I + L P  +     ++     L +I+ED +IIV++KP  +I  P       T++N +   L+  KD++ L  A + HRLDK T+GL VAAK+      L        VS+ YL +  G+  ++    +        +  M I   N   KE IT Y  IE      L+E QL TG+ HQIRVHM SI HP++GD  YNK
  S:    14 INEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNE-----WIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNAL---LHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGTINQPIGRDPTNRTKMAI---NYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNK 244
>gi|16801023|ref|NP_471291.1| hypothetical protein lin1957 [Listeria innocua Clip11262] >gi|16414458|emb|CAC97187.1| lin1957 [Listeria innocua] (302 aa)
Score = 285, Expect = 8.7e-24, Identities = 85/276 (30%), Positives = 133/276 (48%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +  I +E   +   D +     E S S I   +KNGDI VN +    NYK+Q  D ++   R     +  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + VIE+     L+  +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+
  S:     4 ETLIIEESHARERVDKVIAEMMEKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIRYEAR-----EPEELEILAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVIERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQFLHAAKLGFD 273
>gi|170759270|ref|YP_001788292.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str. Loch Maree] >gi|169406259|gb|ACA54670.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str. Loch Maree] (300 aa)
Score = 285, Expect = 8.9e-24, Identities = 77/254 (30%), Positives = 143/254 (56%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +KK   N  +KD++ +  + LS   I K++++G + VN +K     KL ++D ++I++     +++   N       + ++YED +IIV+NK  G++  P K     TL+N I  +  +  +K+ +   L  RLD+ T+GL + AKNQ +   L +  + ++  K Y+ + +G  K+K   +   I+  EE + ++   + +  +E IT Y V+E+    +++ ++L TG+ HQIRVHM+ +GHP+ GD+ Y K
  S:     9 VKKINHNIDIKDYL-REMENLSGRFIRKAVRDGRVFVNKEKVIKKNKLSQDDLIEIYM-----QEDEHQNIEPEDMNIEIVYEDNDIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVR--LVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDER-GQESITTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHPLYGDSLYGK 253
>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 = 285, Expect = 9.2e-24, Identities = 82/271 (30%), Positives = 134/271 (49%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +E  ++++ + + KS      S I   +KNGDI VN +    NYK+Q  D +        I++  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + V+E+     L+  +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+
  S:    14 RERVDKVIAEMMGKS-----RSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY-----EIREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQYLHAAKLGFD 273
>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 = 285, Expect = 1.0e-23, Identities = 93/297 (31%), Positives = 149/297 (50%)
  Q:     5 FIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNY-LEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF-NFDKNHFLHYLNKLNLEVKNIKFK 301
            I ++E N  L  FISK F+E S S   K I++ ++ VN      NYKL+  D++++      IK++  +N       LN++YED+++IV++KP+G++  P       TL N +  +       N  +   + HR+DK T+G+ V AKN      L+      ++ + Y+ L  G  K    T+ + +  N + +I      N   K  IT Y VI +     L++  L TG+ HQIRVHMA I HP++GD  Y  KK  F      L + K+ F +     ++ + ++L    K I FK
  S:     7 LINEDEANSRLDVFISKCFEEKSRSYAQKLIEDKNVLVNGSIKKSNYKLKTGDNVEV-----TIKEDETINIEPEDIKLNILYEDEDVIVIDKPQGMVVHPGNGNYSGTLVNGLLYHCDSLSSINGDVRPGIVHRIDKDTSGVLVVAKNDNAHIILSEQLKEHSMKREYVALVEGIIKDDEGTIDEPLGRNPKDRIKRAVVRN--GKNAITHYEVIRRFNKNTLVKCILETGRTHQIRVHMAHINHPLVGDPMYGFKKQRFKLNGQMLHARKLGFIHPSSKKYMEFQSELPNYYKEILFK 299
>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 = 285, Expect = 1.0e-23, Identities = 94/277 (33%), Positives = 144/277 (51%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKE-LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE--EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN---FGFQFPCLTSYKIKF 277
           M++I +   E+   L  FI +   + +S + I ++IK+G + VN+++   +YKL+  D +   L  +P K E+    L     L +IYEDK+IIVVNK  G++  P       TL N +   +Y   D       L   + HRLDK T+G+ V AKN K    L+  +      K Y+ +  G+ KK   T+   +  N     +I  +D    + K  IT ++VI++ K+  LL     TG+ HQIRVHM  IGHP+LGD  Y +      FG +   L + K+ F
  S:     1 MLEIQVTAREKGWRLDKFIQEKAPDWISRTYIQRAIKSGMVTVNNEEKKPSYKLKNGDVVSFELPEEPKKVEI----LPENLPLKIIYEDKDIIVVNKDPGVVTHPTPTFLSGTLVNAL---MYHCNDFQGIGGELRPGIVHRLDKDTSGVIVVAKNDKAHQSLSMQFKERKTEKTYIAIVSGEVKKNYGTIDVPLGRNPVVRTKIAPVD----WGKNAITYFKVIKRFKNATLLLAFPKTGRTHQIRVHMKYIGHPLLGDELYGRGKKDEIFGVKRQMLHALKLSF 276
>gi|71064834|ref|YP_263561.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter arcticus 273-4] >gi|71037819|gb|AAZ18127.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter arcticus 273-4] (338 aa)
Score = 284, Expect = 1.0e-23, Identities = 80/270 (29%), Positives = 149/270 (55%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPIL-NVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGK----FKKKSDTLKDFIFLNEEKQIMEIDRENKFNKE----IITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKI 275
           + + + +Q L +F+    K L    I K I++ +I+VN+K+   + ++Q  D ++I   +   +++  ++   AK +L  V+YED+ +IV+NKP G+            L+  + + + E   K YLE  L HR+DK T+GL + +K +  L  L      + + K+YLC+  G+     ++    L  +   + E+++ ++D ++   KE    I+   R    ++ ++L+E + LTG+ HQIRVH+A IGH +LGD KY+     G    CL ++++
  S:    38 VTRHQHDQRLDNFLLNRLKGLPKPHIYKMIRSDEIRVNNKRCKAHDRVQREDVVRIAPVVLATREKPIISTEFAKSLLARVVYEDEGLIVLNKPSGIAVHGGSG-----LDFGVIEAMREVTGKKYLE--LVHRIDKDTSGLLMISKKRSALKVLQQHLVDKTIQKHYLCIAKGQPALNEQRIDAPLLRYTLASGERRV-KVDAQDPQTKESQTDIVVHGRFTIAEQPVSLIEAKPLTGRTHQIRVHLAHIGHAILGDNKYHVHDKSGVHRLCLHAWRL 308
>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 = 284, Expect = 1.1e-23, Identities = 82/241 (34%), Positives = 126/241 (52%)
  Q:    19 ISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           I++ F++ S ++I K +K G I VN + T   + +  ++ ++I + L P  +     ++     L +I+ED +IIV++KP  +I  P       T++N +   L+  KD++ L  A + HRLDK T+GL VAAK+      L        VS+ YL +  G+  ++    +        +  M I   N   KE IT Y  IE      L+E QL TG+ HQIRVHM SI HP++GD  YNK
  S:    29 INEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNE-----WIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNAL---LHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGTINQPIGRDPTNRTKMAI---NYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNK 259
>gi|170756838|ref|YP_001782613.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str. Okra] >gi|169122050|gb|ACA45886.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str. Okra] (300 aa)
Score = 284, Expect = 1.1e-23, Identities = 77/254 (30%), Positives = 143/254 (56%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +KK   N  +KD++ +  + LS   I K++++G + VN +K     KL ++D ++I++     +++   N       + ++YED +IIV+NK  G++  P K     TL+N I  +  +  +K+ +   L  RLD+ T+GL + AKNQ +   L +  + ++  K Y+ + +G  K+K   +   I+  EE + ++   + +  +E IT Y V+E+    +++ ++L TG+ HQIRVHM+ +GHP+ GD+ Y K
  S:     9 VKKINHNIDIKDYL-REIENLSGRFIRKAVRDGRVFVNKEKVIKKNKLSQDDLIEIYM-----QEDEHQNIEPEDMNIEIVYEDNDIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVR--LVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDER-GQESITTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHPLYGDSLYGK 253
>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 = 284, Expect = 1.1e-23, Identities = 81/271 (29%), Positives = 134/271 (49%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +E  ++++ + + KS      S I   +KNGDI VN +    NYK+Q  D +        +++  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + V+E+     L+  +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+
  S:    14 RERVDKVIAEMMGKS-----RSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY-----EVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQFLHAAKLGFD 273
>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 = 284, Expect = 1.1e-23, Identities = 82/241 (34%), Positives = 126/241 (52%)
  Q:    19 ISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           I++ F++ S ++I K +K G I VN + T   + +  ++ ++I + L P  +     ++     L +I+ED +IIV++KP  +I  P       T++N +   L+  KD++ L  A + HRLDK T+GL VAAK+      L        VS+ YL +  G+  ++    +        +  M I   N   KE IT Y  IE      L+E QL TG+ HQIRVHM SI HP++GD  YNK
  S:    29 INEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNE-----WIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNAL---LHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGTINQPIGRDPTNRTKMAI---NYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNK 259
>gi|115372593|ref|ZP_01459900.1| ribosomal large subunit pseudouridine synthase C [Stigmatella aurantiaca DW4/3-1] >gi|115370314|gb|EAU69242.1| ribosomal large subunit pseudouridine synthase C [Stigmatella aurantiaca DW4/3-1] (330 aa)
Score = 284, Expect = 1.1e-23, Identities = 78/265 (29%), Positives = 129/265 (48%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI------FLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           MI+  I+++     L  ++ K    +  S + K I+   ++VN K+      L   D + I       L   P  + L        P  L ++ ED  ++ V+KP G+           TL + ++ YL  K  +N   A+  HRLD+ T+G+ + AK +  +     ++      K Y+ L  GK  + S  +   + L+E +Q  E       N +E +T+++VI Q  + ALL   + TG+ HQIR H+A++GHPV GD KY   G+F F
  S:    10 MIEFRIEEDSVGMRLDKYLRKRLANMPTSHLFKMIRVKKVRVNGKRAQPEQLLAAGDVIAIRGDEQQLLGPAPGGERLPPPPPPVDPSELVILLEDDWMMAVDKPSGMAVHTGSGITGGTLVDYVRAYLGPKAVRNDFTASPAHRLDRETSGVILVAKRRPAMVHFTEVFTESRARKRYVTLVKGKMPQDSGVID--LPLSEHQQTAESKARRGVNMQEALTRWKVIRQSSEAALLSCAIETGRTHQIRRHLAAVGHPVAGDRKY---GDFAF 277
>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 = 284, Expect = 1.1e-23, Identities = 93/278 (33%), Positives = 138/278 (49%)
  Q:     6 IKKEEENQILKDFISKSF-KELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNH 283
           ++K E N  L  F+ +   K +S S + ++IK G + VN      NY+++  D ++I      I    +   +E +PI + VIYED++IIVVNKP G+I  P  +    TL N +   LY  KD       L   + HRLDK T+G+ V AKN      L+N +    V K YL L  GK +     ++  I +     +      ++  +  +T Y+VI+  +   LL     TG+ HQIRVHM  I HP+LGD  Y K      Q   L + K+ F   + H
  S:     3 VEKSEVNLRLDLFLLQRIPKAISRSFVQRAIKEGKVTVNDVIRKPNYRVKFGDVVKI-----SIPSNAQSISIEPEPIQIGVIYEDEDIIVVNKPAGMIVHPIPSHNSGTLVNAL---LYHCKDLKGIGGELRPGIVHRLDKDTSGVMVVAKNDFAHHNLSNQFKDRKVFKMYLALVSGKVEHLEGDIQ--ISIARHPVLRTKMAASEIGRIAVTHYKVIKYFEHATLLMAFPKTGRTHQIRVHMKCINHPILGDKLYGKGSGASRQM--LHATKLGFYHPRTH 274
>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 = 284, Expect = 1.1e-23, Identities = 88/286 (30%), Positives = 153/286 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF-NFDKNHFLHYLNKL 291
           + +++  + +  ++++ F + S S I   I+  DIKVN+K    NYKL+  D +++         E ++  +EA+ I +N++YEDK+++VVNKP+G++  P       TL N +   LY  KD       +   + HR+DK T+G+ V AKN +   +L++     ++ + Y  L  G+ K     +   +  N+  ++     E    K  +T Y V+E+     L++  L TG+ HQIRVHMASIG P++GD  Y  KK  F  +   L +  + F +  KN ++ +  +L
  S:     8 VDEKDRGERIDKYLAEIFVDKSRSFIQGLIEKDDIKVNNKTPKSNYKLRALDEIEVTF------SEPEVLRVEAEEIPINILYEDKDVVVVNKPQGMVVHPAPGNYNGTLVNAL---LYHCKDLSSINGIIRPGIVHRIDKDTSGVLVVAKNDEAHNKLSDQLKDHSMKREYYALVEGRLKNDKGIIDKPLARNKRDRLKIGIVEG--GKRAVTHYEVLERFNGYTLIKCILETGRTHQIRVHMASIGFPLVGDPLYGFKKQRFKLKGQVLHAKTLGFVHPSKNEYMEFTTEL 289
>gi|151570931|gb|EDN36585.1| hypothetical protein FTCG_00787 [Francisella tularensis subsp. novicida GA99-3549] (332 aa)
Score = 284, Expect = 1.1e-23, Identities = 82/241 (34%), Positives = 126/241 (52%)
  Q:    19 ISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           I++ F++ S ++I K +K G I VN + T   + +  ++ ++I + L P  +     ++     L +I+ED +IIV++KP  +I  P       T++N +   L+  KD++ L  A + HRLDK T+GL VAAK+      L        VS+ YL +  G+  ++    +        +  M I   N   KE IT Y  IE      L+E QL TG+ HQIRVHM SI HP++GD  YNK
  S:    29 INEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNE-----WIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNAL---LHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGTINQPIGRDPTNRTKMAI---NYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNK 259
>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 = 284, Expect = 1.1e-23, Identities = 86/257 (33%), Positives = 134/257 (52%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           +I +  +   + +   I++ F++ S S+I K IK+G I VN K T   + L  ++ ++I + L P  +     +L     LN+++ED +IIV++KP  ++  P       T++N +  + Y  +DK    A + HRLDK T+GL VAAK+      L    +   VS+ YL +  G+  ++    +        +  M I   N   KE IT Y+ IE      L+E QL TG+ HQIRVHM SI HP++GD  YNK
  S:    13 KIMMHPDHAGKRIDSTINELFEQFSRSQIQKWIKDGLITVNGKTTKSKHILLGDEEVEINIELLPTNE-----WLAEDIDLNIVFEDNDIIVIDKPIDMVVHPGAGNMTGTISNALL-HKYPNQDK-LPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLSERKVSRKYLAIVEGEIYEEGTINQPIGRDLNNRTKMTI---NHKGKEAITHYKPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNK 259
>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 = 284, Expect = 1.2e-23, Identities = 88/271 (32%), Positives = 147/271 (54%)
  Q:     7 KKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           +KE+E + +  F++    + + S I K I +  + VN K    +YK++END + +      I +  K++ L     L+++YED +IIV+NKP+G++  P       TL N +   LY  K+       L   + HRLDK T+G+ V AKN K    L+N     +V K Y+ +  G  K +   ++  I  +  +++ M +  + ++    +T Y+V+E+ K+  L+E  + TG+ HQIRVHMA IGHP++GD  Y  K+  F  +   L S  + F
  S:    12 EKEDEGKRIDVFLAAEL-DYTRSYIKKLIVDELVFVNGKTVKPSYKVKENDEVVV-----NIPEAEKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNAL---LYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKIEAPIGRHPVDRKKMAVIEDGRY---ALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAYIGHPIVGDHVYGFKRQKFKLEGQALHSSVLGF 276
>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 = 284, Expect = 1.2e-23, Identities = 86/263 (32%), Positives = 150/263 (57%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEK-KDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGD-------TKYNKKGN------FGFQFPCLTSYKIKF 277
           +  +++ + ++ S S I K   +G++  N  +   NY+++ +D++++ +       E ++  +E + I L+++YEDK+IIV+NKP+G++  P       TL N + K+  +   D N  +   + HR+DK T+GL V AK+      L+    T  + + Y+ L  G   + S  +   I  N  E++ M ++ EN  N   IT ++V+E+ ++   LE++L TG+ HQIRVHMA I HP++GD        KY  KG         FQ P +T  ++KF
  S:    15 IDSWLAGNLEDYSRSYIQKLCLDGNVWANGIQVKSNYRVKTDDNIKVNV------PEAEILDVEPEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNYTGTLVNALMKHCGDSLSDINGVIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDIKREYIALVDGIIYENSGKIDAPIGRNPVERKKMCVNTENGRNA--ITHFKVLERFQNATYLELKLETGRTHQIRVHMAYINHPIIGDMVYGRRKQKYKTKGQVLHAWRLSFQHP-ITGEEVKF 285
>gi|104773696|ref|YP_618676.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842] >gi|103422777|emb|CAI97416.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842] (302 aa)
Score = 284, Expect = 1.2e-23, Identities = 78/264 (29%), Positives = 137/264 (51%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN--YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRE-NKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQ 266
           ++ + K +  Q+    + K F   +++        G + VNH +   +Y+L+E D +   +  +P+   LK++    +P L+++ E  + +V+NKP GL+  P      D + NR+  Y +EK+  N  Y++ ++  RLD+ T+GL +  KN       + L     + KY+  + +G F +    L   I     +    + RE N   +  +T+YRV+ Q    +L+E++LLTG+ HQIR+HMASIGH + GD  Y  +  F  Q
  S:     5 KMIVAKNDPGQLSHFLLKKGFSRRAVNNCKN--HGGMMLVNHHRRNGSYRLKEGDVVHFLMGQEPVNPWLKVS---RRP-LDIVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLAY-FEKQGVNPAYVKPHIVTRLDQDTSGLVLLGKNAIAHDRFSKLGKDAFIKKYH-AIVHGNFAEGD--LSGLIDKPLARVGDTVKREVNPKGQRALTEYRVLNQVPGASLVELRLLTGRTHQIRIHMASIGHVLYGDDLYGARDAFARQ 261
>gi|116513692|ref|YP_812598.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365] >gi|116093007|gb|ABJ58160.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365] (297 aa)
Score = 284, Expect = 1.2e-23, Identities = 78/263 (29%), Positives = 136/263 (51%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN--YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRE-NKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQ 266
           + + K +  Q+    + K F   +++        G + VNH +   +Y+L+E D +   +  +P+   LK++    +P L+++ E  + +V+NKP GL+  P      D + NR+  Y +EK+  N  Y++ ++  RLD+ T+GL +  KN       + L     + KY+  + +G F +    L   I     +    + RE N   +  +T+YRV+ Q    +L+E++LLTG+ HQIR+HMASIGH + GD  Y  +  F  Q
  S:     1 MIVAKNDPGQLSHFLLKKGFSRRAVNNCKN--HGGMMLVNHHRRNGSYRLKEGDVVHFLMGQEPVNPWLKVS---RRP-LDIVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLAY-FEKQGVNPAYVKPHIVTRLDQDTSGLVLLGKNAIAHDRFSKLGKDAFIKKYH-AIVHGNFAEGD--LSGLIDKPLARVGDTVKREVNPKGQRALTEYRVLNQVPGASLVELRLLTGRTHQIRIHMASIGHVLYGDDLYGARDAFARQ 256
>gi|194336853|ref|YP_002018647.1| pseudouridine synthase, RluA family [Pelodictyon phaeoclathratiforme BU-1] >gi|194309330|gb|ACF44030.1| pseudouridine synthase, RluA family [Pelodictyon phaeoclathratiforme BU-1] (349 aa)
Score = 284, Expect = 1.2e-23, Identities = 75/243 (30%), Positives = 129/243 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL---YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEE--KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +  ++++  +  + +K+ ++I+ G + VN  +   NY+++  D +++   L+P   EL     E  PI  +IYED +++VVNK  G++  P       TL N I  ++    E+ D+  L   + HRLDK T+GL + AKN   L  L   +    V K Y  + +G     + T+   I  +++  K +     E ++ K  IT Y V+E  +  +LL ++L TG+ HQIR H+  +GH +LGD  Y
  S:    36 IDQYLTQQVENATRNKVQEAIEEGRVLVNENRVKSNYRIKSCDVIEMTF-LRPPAPELTA---ENIPI-EIIYEDCDLMVVNKKAGMVVHPAFGNWTGTLANAILHHIGMDAEELDQAELRPGIVHRLDKNTSGLIIVAKNPIALHRLARQFAERKVIKVYKAIVWGVPDPAAGTITTNIGRSKKDRKVMANFPFEGEYGKTAITDYSVMENLQWFSLLSLRLHTGRTHQIRAHLQHLGHQILGDVTY 278
>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 = 284, Expect = 1.3e-23, Identities = 82/243 (33%), Positives = 131/243 (53%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           F+S+    LS + I K IK   + VN K    N  L+  D + + +   P KKE+ L  +     L+++YED  II++NKPR ++  P    +  TL N +  +  +    N     + HRLDK TTGL + AK+ +T  +L  ++    ++K YL +C G F K+ + L D     +EK   ++  ++K  K  IT+Y V+      +L+++ L TG+ HQIRVH +S+ HP++GD  Y KK
  S:    17 FLSEKISNLSRTSIQKLIKGKLVFVNGKNIKPNVILEIGDEITVSI---PDKKEITL--VAEDIDLDIVYEDDYIIIINKPRNMVVHPAVGNEKHTLVNALLNHC-KLSMINSERPGIVHRLDKDTTGLIICAKDDETHLKLVEMFANREINKKYLAICNGSFSKE-NGLIDKPIGRDEKDRKKMSVKSKSGKAAITEYNVLISNLKYSLVDVTLHTGRTHQIRVHFSSLNHPIIGDETYGKK 252
>gi|145219868|ref|YP_001130577.1| ribosomal large subunit pseudouridine synthase D [Prosthecochloris vibrioformis DSM 265] >gi|145206032|gb|ABP37075.1| ribosomal large subunit pseudouridine synthase D [Prosthecochloris vibrioformis DSM 265] (349 aa)
Score = 284, Expect = 1.3e-23, Identities = 79/259 (30%), Positives = 128/259 (49%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKK---DKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSY 273
           +  ++S+  +  + +K+ ++I++G + VN K    NY+++  D +++   L+P   EL     E  PI  ++YED  ++V+NK  G++  P       TL N I  ++ E     D++ L   + HRLDK T+GL + AKN   L  L   +    V K Y  L +G       T++  I  +  + K +     E +  K  IT YR+ E     +LL + L TG+ HQIR HM  +GH +L D  Y         FP   S+
  S:    36 IDQYLSRQVENATRNKVQEAIEDGRVLVNDKVVKSNYRIKSCDLIEMTF-LRPPAPELAP---EDIPIA-IVYEDSELMVINKEPGMVVHPAFGNWTGTLANAILHHIGENAGSLDESELRPGIVHRLDKDTSGLIIIAKNPTALHRLAKQFADRKVVKTYKALVWGVPATPEGTIRTNIGRSRKDRKVMANFPYEGEEGKTAITDYRLEEDLHWFSLLSLTLHTGRTHQIRAHMQHLGHQILSDATYGGASIRNLDFPKSESF 294
>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 = 284, Expect = 1.3e-23, Identities = 82/268 (30%), Positives = 140/268 (52%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKK-TTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           M Q+ ++   + + L  ++     +LS S++ K I+ G I++N +  T  N K+ + D L+I +   P  + L+L    A+ I L+++YED  +I++NKP  L+  P    +  TL N +  +         ++   + HRLDK TTG  V AK  +    L     T+   + Y+ L +G  K ++ T+   I  +  ++Q M I    K  +  +T ++V E+  +  L+E +L TG+ HQIRVH + IGHP+LGD  Y+   + G   P
  S:     1 MNQLNLEVAGKKERLDAWMGSHLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQGDRLKITI---PDSQPLELT---AEAIELDILYEDDYLIIINKPADLVVHPAPGHESGTLVNALLHHCPNLAGIGGIQRPGIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYIALVHGVPKSETGTIDLPIGRHRSDRQKMAIIAVEKGGRNAVTHWQVKERLGNYTLMEFRLETGRTHQIRVHSSHIGHPILGDPLYSSGRSIGINLP 266
>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 = 283, Expect = 1.4e-23, Identities = 81/271 (29%), Positives = 134/271 (49%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +E  ++++ + + KS      S I   +KNGDI VN +    NYK+Q  D +        +++  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + V+E+     L+  +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+
  S:    14 RERVDKVIAEMMGKS-----RSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY-----EVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQFLHAAKLGFD 273
>gi|93005114|ref|YP_579551.1| pseudouridine synthase, RluD [Psychrobacter cryohalolentis K5] >gi|92392792|gb|ABE74067.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter cryohalolentis K5] (343 aa)
Score = 283, Expect = 1.4e-23, Identities = 80/270 (29%), Positives = 150/270 (55%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPIL-NVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGK----FKKKSDTLKDFIFLNEEKQIMEIDRENKFNKE----IITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKI 275
           + + + +Q L +F+    K L    I K I++ +I+VN+K+   + ++Q  D ++I   +   +++  ++   AK +L  V+YED+ +IV+NKP G+            L   + + + E   K YLE  L HR+DK T+GL + +K +  L  L      + + K+YLC+  G+     ++   +L  +   + E+++ ++D ++   KE    I+   R +  ++ ++L+E + LTG+ HQIRVH+A IGH +LGD KY+     G    CL ++++
  S:    43 VTRHQHDQRLDNFLLNRLKGLPKPHIYKMIRSDEIRVNNKRCKAHDRVQREDVVRIAPVVLATREKPIISTEFAKSLLARVVYEDEGLIVLNKPSGIAVHGGSG-----LAFGVIEAMREVTGKKYLE--LVHRIDKDTSGLLMISKKRSALKVLQQHLVDKTIQKHYLCIAKGQPALNEQRIDASLLRYTLASGERRV-KVDTQDPQTKESQTDIVVHGRFMIAEQPVSLIEAKPLTGRTHQIRVHLAHIGHAILGDDKYHVHDKSGVHRLCLHAWRL 313
>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 = 283, Expect = 1.4e-23, Identities = 81/271 (29%), Positives = 134/271 (49%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +E  ++++ + + KS      S I   +KNGDI VN +    NYK+Q  D +        +++  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + V+E+     L+  +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+
  S:    14 RERVDKVIAEMMGKS-----RSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY-----EVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQFLHAAKLGFD 273
>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 = 283, Expect = 1.4e-23, Identities = 82/241 (34%), Positives = 126/241 (52%)
  Q:    19 ISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           I++ F++ S ++I K +K G I VN + T   + +  ++ ++I + L P  +     ++     L +I+ED +IIV++KP  +I  P       T++N +   L+  KD++ L  A + HRLDK T+GL VAAK+      L        VS+ YL +  G+  ++    +        +  M I   N   KE IT Y  IE      L+E QL TG+ HQIRVHM SI HP++GD  YNK
  S:    29 INEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNE-----WIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNAL---LHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGTINQPIGRDPTNRTKMAI---NYRGKEAITYYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLVGDQTYNK 259
>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 = 283, Expect = 1.5e-23, Identities = 81/271 (29%), Positives = 134/271 (49%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +E  ++++ + + KS      S I   +KNGDI VN +    NYK+Q  D +        +++  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + V+E+     L+  +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+
  S:    14 RERVDKVIAEMMGKS-----RSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY-----EVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQFLHAAKLGFD 273
>gi|52841563|ref|YP_095362.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella pneumophila subsp. pneumophila str. Philadelphia 1] >gi|52628674|gb|AAU27415.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella pneumophila subsp. pneumophila str. Philadelphia 1] (321 aa)
Score = 283, Expect = 1.6e-23, Identities = 82/261 (31%), Positives = 122/261 (46%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           Q+ + +E  NQ +   +++   E S S I   IK G + +N+       K    D + I +    +  +      E  PI  +IYED  +IVVNKP GL+  P    K  TL N +  +  E +      A + HRLDK TTGL + AKN  + T L        + ++YL L +G           F    + +  M +     F ++ +T Y + +  KD  LL + L+TG+ HQIRVHM  I HPV+GD  Y  +  F
  S:     8 QLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLITINVDHTIVNTDFNYCKPENIPI-QIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQ--LLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHPKNRLKMAV---TDFGRQAVTHYNINKHYKDFTLLNVSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKF 262
>gi|163786072|ref|ZP_02180520.1| ribosomal large subunit pseudouridine synthase D [Flavobacteriales bacterium ALC-1] >gi|159877932|gb|EDP71988.1| ribosomal large subunit pseudouridine synthase D [Flavobacteriales bacterium ALC-1] (343 aa)
Score = 283, Expect = 1.6e-23, Identities = 73/229 (31%), Positives = 122/229 (53%)
  Q:    29 SKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFL---NEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +KI  + K+G I +N+     NYK++ ND + +  +  P +     N L A+ I ++V+YED +++VVNKP G++  P       TL N +  +     + +     L HR+DK T+GL V AK ++ +  L+N +  +   + Y+ L +G   +    ++  I     N  +  + +D E    K  IT Y+VIE+   + L+  +L TG+ HQIRVHM  IGH +  D +Y
  S:    45 NKIQSAAKDGCIFINNSPVKSNYKVKPNDFVTVKFKHPPHE-----NLLIAEDIPIDVVYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALIFHFENLPNNSSDRPGLVHRIDKDTSGLLVVAKTEQAMAHLSNQFAKKTSEREYVALVWGNMTEDEGIIEGNIGRHPKNRLQNTVYLDDEADKGKPAITHYKVIERLGYVTLVSCKLETGRTHQIRVHMKHIGHTLFNDARY 272
>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 = 283, Expect = 1.7e-23, Identities = 77/261 (29%), Positives = 134/261 (51%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKP---ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN 262
           ++  I   E+N  +  ++++   +LS S + K +K+G + VN +    NYK Q  D   + L +  ++        + KP    L+++YED+ ++VVNKP+ ++  P       TL N +  +  +        +   + HR+DK TTG  +  K+      L       ++ + Y  +  G  K+   T+   I  +  +++ M I+ +N   KE +T Y+V+E+      +E +L TG+ HQIRVHMAS+GHP+LGDT Y    N
  S:     4 LEFNIDSSEKNVRIDKYLAECCPDLSRSYLQKLLKDGAVSVNTRIVKANYKTQPGD--HVILNIPDLQTP------DIKPENIPLDILYEDQWLMVVNKPKDMVVHPSAGHMEGTLVNAVMAHCGDNLSGINGVMRPGIVHRIDKDTTGALLICKDDMVHRNLAEQLKEHSIKRRYRAIVQGNIKEDEGTVDAPIGRHPIDRKKMAINHKN--GKEAVTHYKVLERFGQTTYIECRLETGRTHQIRVHMASLGHPLLGDTVYGSSKN 260
>gi|75675586|ref|YP_318007.1| pseudouridine synthase, RluD [Nitrobacter winogradskyi Nb-255] >gi|74420456|gb|ABA04655.1| ribosomal large subunit pseudouridine synthase C [Nitrobacter winogradskyi Nb-255] (412 aa)
Score = 282, Expect = 1.9e-23, Identities = 82/265 (30%), Positives = 135/265 (50%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILN-----VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFL--NEEKQIMEIDRE-NKFNKEIITKYRVIE-QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           + +  +E N  +  F+   F  LS S I + ++ G+++VN ++     ++ E D ++I  L+L   K  + L+  E K I +     V++ED +++V+NKP GL  Q         L+  I   L   +D       L HRLD+ T G  + AK +   T L   +   +  K Y  L  G  K K   +  ++    NEE+ IM I    ++     +T Y V+E   + +A + ++ +TG+ HQ+R HMA IGH ++GD KY  K N  +Q P
  S:    89 VAVTADEANMRVDRFLEARFPGLSFSHIQRVVRKGELRVNGRRADSKDRVSEGDKVRIPPLKLDTPKAAVGLSDAETK-IRDELRKMVLFEDADVMVLNKPAGLAVQGGSG-----LSRHIDGMLETMRDAKGQRPRLVHRLDRETAGCLLIAKTRFAATALTGAFRHRSARKIYWALVAGVPKPKQGRISTYLAKEENEEESIMRIAAHGDEGASHAVTYYAVVETSAQKLAWVSLKPVTGRTHQLRAHMAHIGHAIIGDPKYFNKEN--WQLP 355
>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 = 282, Expect = 2.0e-23, Identities = 75/246 (30%), Positives = 128/246 (52%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           F+S      + S I + I++G+I V+ ++   + KL+  +S+ I L      + L     E+ P L V+YED ++IV+NKP G++  P       TL N +  +  +       L   + HRLDK T+G+ V AKN ++   L+  ++  ++ + Y  L YG  ++ S  L+  I  +   ++       +  K  +T++RV  +   + L+E++L TG+ HQIRVHM+  G P+LGD  Y   G F
  S:    17 FLSSQLASETRSTIQRLIESGNIMVDGREVRPSLKLKGGESISIQLPEPVAARPLP----ESIP-LEVLYEDGDLIVINKPAGMVVHPGPGNSSGTLVNALLAHCTDLSGIGGELRPGIVHRLDKGTSGVMVVAKNDRSHQALSAQFSVHSIKRIYQALVYGSPQQDSGRLEGQIGRHPTDRLRRSGLARQ-GKHAVTRWRVRGRYGRICLMELRLETGRTHQIRVHMSEAGFPLLGDPLYPDGGRF 257
>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 = 282, Expect = 2.0e-23, Identities = 83/255 (32%), Positives = 127/255 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN------KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I KE  N++ K        ELS S+ +++IK G + VN K     Y ++E D +   L      +E  L +      L++IYED ++ VVNKP+G++  P       TL N +   +Y  KD       +   + HR+DK T+GL + AKN K    L      +   + Y+ + +G        +        E  I   D++ K        K  +T++ V+E+  +  L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:     4 IIKEAGNRLDKSL--ADLTELSRSQANEAIKAGTVLVNGKSAKAKYVVKEGDVITYVL-----PEEEVLEYKAEDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNAL---MYHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVI--------EAPIGRSDKDRKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR 250
>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 = 282, Expect = 2.0e-23, Identities = 73/238 (30%), Positives = 119/238 (50%)
  Q:    23 FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI---FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           F + S S+I   I++G + VN K+    YKL   D +QI       ++  K++       L+++YED ++IVVNKP+G++  P       TL N +  +             + HR+DK T+GL + AKN      L      +   + Y+ L +G  K+   T+   +     + +KQ + +D      +  +T + V+E+ K+  L+  QL TG+ HQIRVHM  IGHP+ GD  Y  +
  S:    25 FDQFSRSQIQHWIEDGHVLVNGKQVKPKYKLLVGDHVQII-----PEEPQKIDLAPEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPLGRSLKDRKKQAVVVD-----GRHAVTHFNVLERFKNYTLVACQLETGRTHQIRVHMKYIGHPLAGDPLYGPR 255
>gi|25011477|ref|NP_735872.1| hypothetical protein gbs1435 [Streptococcus agalactiae NEM316] >gi|24413015|emb|CAD47094.1| unknown [Streptococcus agalactiae NEM316] (296 aa)
Score = 282, Expect = 2.0e-23, Identities = 76/236 (32%), Positives = 120/236 (50%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN------KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ELS S+ ++ IK G + VN +     Y +QE D +        I KE  L++      L++IY+D ++ VVNKP+G++  P       TL N +  ++ +    N  +   + HR+DK T+GL + AKN +    L      +   + YL + +G        +        E  I   D++ K        K  IT++ V+E+  D  L+E+ L TG+ HQIRVHMA IGHP+ GD+ Y  +
  S:    21 ELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITF-----DIPKEEVLDYQAENISLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVI--------EAPIGRSDKDRKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHPLAGDSVYGPR 250
>gi|146318440|ref|YP_001198152.1| YlyB [Streptococcus suis 05ZYH33] >gi|145689246|gb|ABP89752.1| YlyB [Streptococcus suis 05ZYH33] (309 aa)
Score = 282, Expect = 2.1e-23, Identities = 77/236 (32%), Positives = 128/236 (54%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELN-NLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +LS S  ++ IK G + VN +     Y +Q  D L        I +  +++++     L ++++D+++ VVNKP+G++  P       TL N +   LY  KD       L   + HR+DK T+GL + AKN    T+L   L + +++ KY+  + +G        ++  I  +E+      DR+ +      KE +T+++V+E+  D  L+E+ L TG+ HQIRVHMA IGHPV GD  Y  +
  S:    21 DLSRSVANEQIKAGQVLVNGQPKKAKYSVQVGDVLTY-----QIPEVEEIDYVAEDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL---LYHVKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYW-AIVHGNLPNDRGVIEAPIGRSEK------DRKKQAVTAKGKEAVTRFQVLERFGDYTLVELTLETGRTHQIRVHMAYIGHPVAGDEAYGPR 250
>gi|167344070|ref|ZP_02289911.1| hypothetical protein LmonocyFSL_13863 [Listeria monocytogenes FSL J1-208] (328 aa)
Score = 282, Expect = 2.1e-23, Identities = 81/271 (29%), Positives = 135/271 (49%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +E  ++++ + + KS      S I   +KNGDI VN +    NYK+Q  D +        +++  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + V+E+     L++ +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+
  S:    14 RERVDKVIAEMMGKS-----RSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY-----EVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVLERLPGYTLIKCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQFLHAAKLGFD 273
>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 = 282, Expect = 2.1e-23, Identities = 86/259 (33%), Positives = 140/259 (54%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL----EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEID------RENKFN------KEIITKYRVIEQ--KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++  + +E+  + L  F++K++ ELS S I + I+ G   V  K    +Y+++E D + + +  +P   E+K    E  PI  V+YED++++V+ KP GL+  P       TL N +   LY  KD + +       + HRLDK T GL V AKN  +   L   + +    K Y  L  G  K             EE  I+E+          KF+      K   +++ V+E+    ++ LL++++ TG+ HQIRVH++SIGHP++GDT Y  K
  S:     8 LEFTVSEEQAGERLDTFLAKAYPELSRSYIKRLIEEGFALVEGKVRKPSYRVKEGDRVTLSVP-EPEPLEVKP---EDIPI-EVVYEDRDVVVIVKPCGLVVHPSPGYTSGTLVNAL---LYHIKDLSSIGGVERPGIVHRLDKETAGLMVVAKNDTSHRNLVEQFASRRTEKLYRALVKGTVK-------------EEHGILELPIGRHPFHRKKFSTSSPRSKPAKSEFWVLERFPGLELTLLKVKIYTGRTHQIRVHLSSIGHPIVGDTTYGFK 263
>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 = 282, Expect = 2.2e-23, Identities = 78/258 (30%), Positives = 126/258 (48%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN------KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKN 282
           ELS S+ ++ IK G + VN +     Y +QE D +        I K+  L++      L++IY+D ++ VVNKP+G++  P       TL N +  ++ +    N  +   + HR+DK T+GL + AKN +    L      +   + YL + +G        +        E  I   D++ K        K  +T++ V+E+  D  L+E+ L TG+ HQIRVHMA IGHP+ GD  Y  +   G +   L +  + F    N
  S:    21 ELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITF-----DIPKKEVLDYQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDQGVI--------EAPIGRSDKDRKKQAVTAKGKPAVTRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHPLAGDPVYGPRKTLGGKGQFLHAQTLGFTHPSN 272
>gi|146306004|ref|YP_001186469.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas mendocina ymp] >gi|145574205|gb|ABP83737.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas mendocina ymp] (324 aa)
Score = 282, Expect = 2.2e-23, Identities = 76/256 (29%), Positives = 127/256 (49%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +Q  +  E+  Q L    ++ F E S S++S  IK+G + V+         +    +L +       ++E +  ++     LN++YED++++V++KP GL+  P       TL N +   L+   D  N   A + HRLDK TTGL V AK  +  T L       +VS+ Y C+C G               + ++Q M +       K  I+ YRV+E+ +    + ++L TG+ HQIRVHM+ +G+P++GD  Y
  S:    11 LQAIVPFEQGGQRLDQVAAQLFGEFSRSRLSTWIKDGRLTVDGAVARPRDTVHAGSTLVL-----DAEQEAQGEWVAQDIELNIVYEDEHLLVIDKPAGLVVHPAAGHADGTLLNAL---LHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTLQAQTNLVEQLQKRSVSRIYECICIGVITAGGTIDAPIGRSSSQRQRMAV---TDGGKPAISHYRVLERYRSHTHVRVKLETGRTHQIRVHMSHVGYPLVGDPVY 256
>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 = 282, Expect = 2.2e-23, Identities = 86/264 (32%), Positives = 141/264 (53%)
  Q:     5 FIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKEL-KLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENK----FNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK------KGNF------GFQFP 268
           FI KEE  + L   +++    ++ S I + IK G++ VN +    NYK+Q +D + I      I+ EL  L  L     + ++Y+D++++VVNK +G++  P    +  TL N +   +Y  KD       +   + HR+DK T+GL + AKN     +L      +   + Y+ L +G    +  T+     L   K    +DR+ +      +E +T + V+E+ KD  L+ ++L TG+ HQIRVHM  IG+P+ GD  Y        KG F      GF+ P
  S:     7 FIIKEETGR-LDKVLTELLPSITRSHIQQWIKEGNVTVNGENLKANYKVQPSDEIVI------IEPELVSLEVLAEDIPIEIVYQDEDVVVVNKAQGMVVHPSAGHQTGTLVNAL---MYHIKDLSGINGTIRPGIVHRIDKDTSGLLMVAKNDSAHEKLAAQLKDKTSLREYIALVHGVIPHEKGTID--APLGRSK----VDRKKQDIIDGGREAVTHFTVLERFKDFTLVSLKLETGRTHQIRVHMKYIGYPLAGDPIYGPRKTLEGKGQFLHAQTLGFKHP 275
>gi|31364860|gb|AAP49462.1| YlyB [Streptococcus suis] (297 aa)
Score = 282, Expect = 2.3e-23, Identities = 77/236 (32%), Positives = 128/236 (54%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELN-NLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +LS S  ++ IK G + VN +     Y +Q  D L        I +  +++++     L ++++D+++ VVNKP+G++  P       TL N +   LY  KD       L   + HR+DK T+GL + AKN    T+L   L + +++ KY+  + +G        ++  I  +E+      DR+ +      KE +T+++V+E+  D  L+E+ L TG+ HQIRVHMA IGHPV GD  Y  +
  S:    21 DLSRSVANEQIKAGQVLVNGQPKKAKYSVQVGDVLTY-----QIPEVEEIDYVAEDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL---LYHVKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYW-AIVHGNLPNDRGVIEAPIGRSEK------DRKKQAVTAKGKEAVTRFQVLERFGDYTLVELTLETGRTHQIRVHMAYIGHPVAGDEAYGPR 250
>gi|87123536|ref|ZP_01079387.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9917] >gi|86169256|gb|EAQ70512.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9917] (329 aa)
Score = 281, Expect = 2.4e-23, Identities = 82/256 (32%), Positives = 134/256 (52%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S ++I K I  G ++VN K       L++ D++Q+++   P  + L   +L+ +P+ L+V++ED+++IV+NKP GL   P    K  TL N +   L+   D       L   + HRLDK TTG  V AK+Q+ L +L         S+ YL + +G  +  S T+   I  +  + K+   +  EN   +   T + + E+  D +LL  +L TG+ HQIRVH A + HPV+GD  Y++      + P    +  +   D
  S:    49 EQSRARIQKFIDAGFVRVNGKTGKAKTPLRQGDAVQLWM---PPPEPLP--YLKPEPMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGL---LHHCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQLQIQKRIASREYLAVVHGVPRGDSGTIVGAIGRHPADRKKYAVVSGEN--GRYACTHWSLQERLADYSLLRFKLDTGRTHQIRVHCAHMNHPVVGDPTYSRCRKLPVELPGQALHAFQLGLD 301
>gi|42525117|ref|NP_970497.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100] >gi|39577328|emb|CAE81151.1| Pseudouridylate synthase [Bdellovibrio bacteriovorus HD100] (319 aa)
Score = 281, Expect = 2.5e-23, Identities = 71/229 (31%), Positives = 127/229 (55%)
  Q:    29 SKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDF-------------IFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           S+ S  +++  + +N K    +  ++END ++I L   P  +  +L   + K  L+V++ED+++IV+NKP GL+  P      DTL N +  +  +   K   E   + HRLDK T+G+ V AKN K    L + +   +  + Y  +C G  +  S +++ F             +  ++ K + + + +    K  +T + V+++K  M+ L+++L TG+ HQIRVHM+  G P+ GDT Y
  S:    20 SRASHLLESNSVLLNGKPAKASVAIKENDLIEIQL---PEPEPTELQPFDLK--LDVLFEDEDLIVINKPAGLVVHPAAGHAHDTLVNALIHHTDDLSMKFGEERPGIVHRLDKETSGIIVIAKNDKAHESLTSQFKERSTHRIYYAVCLGTARTLSGSVRSFLARHPVDRKRYASVLGDDRKPLTDPNDDPGLGKWAVTHFEVLQRKSGMSYLKLKLETGRTHQIRVHMSESGLPIAGDTLY 257
>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 = 281, Expect = 2.5e-23, Identities = 91/296 (30%), Positives = 153/296 (51%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKFNFDKN-HFLHYLNKLNLEVKNI 298
           +  +K+E EN+ L  FI ++ K+ S S I K   +  I VN +    NYK++  D +++ L      KE  +   +    LN++YED++IIV+NKP+G++  P       TL N +  +     + N  E   + HR+DK T+G+ V AK  +    L N     ++ + Y+ L  G  K+   T+   +  N   +I     +    K  +T Y+VI +  + +L+E +L TG+ HQIRVHM+ IGHP++GD  Y  K+  F  +   L + K+ F    N  ++ + +++  E K I
  S:     7 KFLVKEEFENERLDLFIVENLKDKSRSFIKKLSDDKGIMVNDEIKKVNYKVKCGDIVKVLL-----PKEEGIYLEKENMDLNILYEDEDIIVINKPQGMVVHPGVGNTKGTLVNGLLAHCKSLSNINGEERPGIVHRIDKDTSGILVIAKTNRAHEHLANQLKDHSMLRVYMALTEGVIKEDMGTIDKDLGRNPSDRIKFAVVDE--GKRAVTHYKVINRYNNNSLIECRLETGRTHQIRVHMSYIGHPIVGDPTYGYKRQKFKLKGQMLHAKKLGFIHPTNGEYMEFDSEIPEEFKKI 298
>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 = 281, Expect = 2.6e-23, Identities = 80/255 (31%), Positives = 131/255 (51%)
  Q:     6 IKKEEENQILKDFISKSFKE-LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDREN----KFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I +EEE  +  D +    +E  S S++ + IK+G++KVN  +   NYK    D + I      I +  +L+ +     L++ +ED ++IVVNKPRG++  P       TL N +  +  +    N  L   + HR+DK T+GL + AKN     +L      + V++ Y  + +G       T+ D     + K     DR+N       ++ +T + V+E+  D   +E +L TG+ HQIRVHM  IG+P+ GD KY  +
  S:     7 IVREEEKSVRLDKVLTQLEEKWSRSQVQQWIKDGNVKVNGSQVKTNYKCAIEDKIII-----SIPEPEELDVVPENMDLDIYFEDADVIVVNKPRGMVVHPAPGHPSGTLVNGLMAHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDLAHEKLVEQLVNKTVTRKYKAIVHGIIPHDHGTI-DAPLGRDPK-----DRQNMAVVDSGRDAVTHFNVLERFTDFTYVECKLETGRTHQIRVHMKYIGYPLAGDPKYGPR 256
>gi|167214706|ref|ZP_02285013.1| ribosomal large subunit pseudouridine synthase, RluD subfamily protein [Listeria monocytogenes FSL R2-503] (329 aa)
Score = 281, Expect = 2.6e-23, Identities = 81/271 (29%), Positives = 134/271 (49%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +E  ++++ + + KS      S I   +KNGDI VN +    NYK+Q  D +        +++  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + V+E+     L+  +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+
  S:    14 RERVDKVIAEMMGKS-----RSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY-----EVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQFLHAAKLGFD 273
>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 = 281, Expect = 2.7e-23, Identities = 72/231 (31%), Positives = 119/231 (51%)
  Q:    27 SLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           S + +++ +++G I VN  +   +YK+   D + I   L P  +  ++   E  P L++IYED +++VVNKP+G++  P       TL N +  +             + HR+D+ T+GL + AKN K    L+         + Y  L  G+F + S T+      N      ++DR+ +      +E IT + V+ +     LL+I+L TG+ HQIRVHM  IGHP++GD  Y
  S:    28 SRTVLAEWLQDGHIVVNQTQVKRSYKVNSGDLITI---LPPAVQNTEI-IAENMP-LDIIYEDNDLLVVNKPQGMVVHPAAGHTSGTLVNALLYHAPLSTINGSFRPGIVHRIDRDTSGLLMVAKNDKAHQALSEQLKAHKNERIYYALVRGEFSEDSGTI------NAPLARHKVDRKKQAVQAGGREAITHFEVVTRYVGYTLLKIRLETGRTHQIRVHMTYIGHPIIGDPVY 251
>gi|27262446|gb|AAN87504.1| Ribosomal large subunit pseudouridine synthase D [Heliobacillus mobilis] (327 aa)
Score = 281, Expect = 2.8e-23, Identities = 81/243 (33%), Positives = 129/243 (53%)
  Q:    35 IKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQ--KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           IK G IKV       NY+L+  D +++ +  +P+  E+     E  PI +++Y+D ++ V+NK  GL+  P +     TL N +   LY  KD       L   + HR+DK T+GL V AK+ +    L        V + YL + +G    ++  +   I  + +++Q M +    K +   +T  RV+E+  +   +L+   L TG+ HQIRVHMA IGHPV GD KY  KK  FG +   L ++++ F
  S:    58 IKEGLIKVEGMTVKANYRLRPGDRIEV-VPAEPVSTEI---IPENIPI-DIVYQDAHVAVINKSAGLVVHPAEGHTSGTLVNAL---LYHIKDLSGINGELRPGIVHRIDKDTSGLLVVAKHDEAHIHLAEQVKDHLVRREYLAIVHGIIGAETGRIDAPIGRDPKDRQKMAVVSSGKAS---VTHLRVLERFPESGFSLVRCNLETGRTHQIRVHMAYIGHPVAGDPKYGPKKAAFGLEGQALHAHRLDF 297
>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 = 281, Expect = 2.9e-23, Identities = 76/262 (29%), Positives = 137/262 (52%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK--NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN 262
           M +I +   E    +  ++    K+ S S I K I +G I VN K    NYK+++ND +     L  I +   L+ +     + ++YED++IIVV+KP+G++  P       TL N + K+           +   + HR+DK T+G+ V AK+      L+       + + Y+ + +G  ++    +   I  +  +++ M ++ +N   +  +T+++V+E+ KD   +E  L TG+ HQIRVHM+ IG P++GDT Y +K +
  S:     1 MEEIILVSNESGIRIDAWLCGKVKDYSRSYIQKLINDGMILVNGKPVKSNYKIKQNDEI-----LARIPEPQVLDVVAEDIDVPILYEDEHIIVVDKPKGMVVHPAAGNYSGTLVNALLKHCGTNLSNINGIIRPGIVHRIDKDTSGVLVVAKSNAAHEGLSEKLKDHDIERVYIAVVHGIIREDYGKIDAPIGRHPVDRKKMAVNTKN--GRRAVTRFKVLERFKDATYIEATLETGRTHQIRVHMSYIGFPIIGDTVYGRKND 258
>gi|148652292|ref|YP_001279385.1| RluA family pseudouridine synthase [Psychrobacter sp. PRwf-1] >gi|148571376|gb|ABQ93435.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter sp. PRwf-1] (364 aa)
Score = 281, Expect = 3.0e-23, Identities = 87/270 (32%), Positives = 151/270 (55%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-----LRLKPIKKELKLNFLEAKPILN-VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGK-----FKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKK----DMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKI 275
           + + +  Q + +F+    K +  + I K I++ ++++N+K+      L+  D ++I       R KP+  E    F  AK +L  V+YED+ +IV+NKP G+            L+  + + + +   K YLE  L HR+DK T+GL + AK + TL  L      + + K+YLCL  G+     F+  +  L+ +   N E+++ ++D+ N   K   T  +V+ + K     ++L+E    TG+ HQIRVH+A +GHP+LGD KYN K   G +  CL ++++
  S:    67 VTRNQHGQRIDNFLLARLKGMPRAHIYKMIRSDEVRINNKRCKPYDNLERGDVVRIAPVKLATREKPVISE---GF--AKSLLERVVYEDEGLIVLNKPSGMAVHGGSG-----LDFGVIEAMRDATSKKYLE--LVHRIDKDTSGLLMIAKKRSTLKVLQEYLREKTIQKHYLCLVKGQPALNEFEIDAPLLR-YTVANGERRV-KVDKANPEAKLSQTTCKVLARFKMNGEPVSLIEAMPHTGRTHQIRVHLAYLGHPILGDDKYNIKDTSGVRRLCLHAWQL 337
>gi|168334458|ref|ZP_02692629.1| putative pseudouridylate synthase [Epulopiscium sp. 'N.t. morphotype B'] (304 aa)
Score = 281, Expect = 3.0e-23, Identities = 78/242 (32%), Positives = 130/242 (53%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           F+++   + + S I K I+ G + +N K      +++  D+++ F    P  +E+ +   E K  L++IYED +I++VNKP+ ++  P      DTL N +   L+  KD        +   + HR+DK TTGL + AKN  +   L++L     + + Y  L YG  K+   T+   I  N + +      EN   +  +T+ RV+E+  +   +E+ L TG+ HQIRVH+ SIGHP+LGD  Y +
  S:    20 FLTEQLPQYTRSYIQKQIELGLLLINGKVAPARTRIKTGDTIE-FTIAPP--REVDITPSEIK--LDIIYEDSDILIVNKPKNMVVHPSAGHYNDTLVNAL---LFYAKDSLSGINGEIRPGIVHRIDKDTTGLLMVAKNDHSHVFLSDLLKDHNIERKYNALVYGNIKEDFFTIDRPIARNPKDRKKMAIVEN--GRRAVTECRVLERFGNATHIELSLQTGRTHQIRVHLTSIGHPLLGDPLYGR 256
>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 = 281, Expect = 3.0e-23, Identities = 83/290 (28%), Positives = 148/290 (51%)
  Q:    12 NQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDREN-KFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKFK 301
           ++ L +FI K+ +    +KI ++ KNG+I+VN      N+K++ ND +++     P +  L     E  P L++++ED  ++VVNKP G++  P       TL N +  +     + +     L HR+DK T+GL V AK ++ +T L   +  +   + Y+ + +G  ++   T++  I  + + ++     E+    KE +T Y+V+E+   +  +  +L TG+ HQIRVHM  IGH +  D +Y   G+   +    T YK    F +N F   L +  L  K + F+
  S:    34 DKFLMNFIEKATR----NKIQQAAKNGNIQVNGAVVKQNHKVKANDVVRVLFEHPPYEFLLTP---EDIP-LDIVFEDDTLLVVNKPAGMVVHPGHGNYSGTLINALIYHFDNLPENSSGRPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSEREYIAIVWGNVEEDQGTVEGHIGRHPKNRMQNTVYEDGDQGKEAVTHYKVLERLGYVTKISCKLETGRTHQIRVHMKHIGHTLFNDERYG--GDAILKGTTFTKYK---QFVENCF-KVLPRQALHAKTLGFE 310
>gi|78189580|ref|YP_379918.1| pseudouridine synthase, RluD [Chlorobium chlorochromatii CaD3] >gi|78171779|gb|ABB28875.1| ribosomal large subunit pseudouridine synthase D [Chlorobium chlorochromatii CaD3] (363 aa)
Score = 280, Expect = 3.1e-23, Identities = 78/256 (30%), Positives = 134/256 (52%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL---YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEE--KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I + + + +    +  ++++  +  + +K+ ++I+ G + VN K    NY+L+  D +++   L+P   EL     EA PI  ++YED +++V+NK  G++  P       TL N I  +L    E  D + +   + HRLDK T+GL + AKN   L +L   +    V K Y  L +G  K+ S T+   I  + +  K +     E    K  IT Y V E  +  +++ ++L TG+ HQIRVH+  +G P++GD  Y
  S:    37 ITLHVSRTQSPMRIDVYLTQQVENATRNKVQEAIEEGRVVVNGKCVKANYRLKSCDVIEVTF-LRPPAPELAP---EAIPIA-IMYEDDDLMVINKEPGMVVHPAFGNWTGTLANAILHHLGNSAEALDASEMRPGIVHRLDKDTSGLIIIAKNPIALHKLARQFAERKVGKIYKALTWGVPKQASGTITTNIGRSHKNRKVMANFPFEGLEGKTAITDYCVEENLEWFSVMSLRLHTGRTHQIRVHLQHLGLPIVGDVTY 292
>gi|78185708|ref|YP_378142.1| pseudouridine synthase, RluD [Synechococcus sp. CC9902] >gi|78170002|gb|ABB27099.1| ribosomal large subunit pseudouridine synthase D [Synechococcus sp. CC9902] (339 aa)
Score = 280, Expect = 3.1e-23, Identities = 81/256 (31%), Positives = 133/256 (51%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF---LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S ++I K I  G ++VN K+      L+E D +Q+++   P  + L   +L+ +P+ L+V++ED++IIV+NK  GL   P    K  TL N +   L+   D       L   + HRLDK T+G  V AK+Q+ L +L         S+ Y  + +G     S T+   +    ++ +K  +  D   ++ +   T + +IE+  D +LL  +L TG+ HQIRVH A I HPV+GD  Y++        P    + ++   D
  S:    52 EQSRARIQKFIDAGYVRVNGKQGKAKTPLREGDQVQLWM---PPPEPLP--YLKPQPMDLDVLFEDEHIIVLNKSAGLTVHPAPGNKDGTLVNGL---LHHCPDLPGISGKLRPGIVHRLDKDTSGCIVVAKSQEALVKLQVQIQKRVASREYFAVVHGVPDGDSGTIIGAVGRHPVDRKKYAVVSDESGRYAR---THWTLIERFGDYSLLRFKLDTGRTHQIRVHCAHINHPVVGDPTYSRCRKLPLDLPGQALHAVQLGLD 304
>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 = 280, Expect = 3.5e-23, Identities = 73/238 (30%), Positives = 119/238 (50%)
  Q:    23 FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI---FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           F + S S+I   I++G + VN K+    YKL   D +QI       ++  K++       L+++YED ++IVVNKP+G++  P       TL N +  +             + HR+DK T+GL + AKN      L      +   + Y+ L +G  K+   T+   +     + +KQ + +D      +  +T + V+E+ K+  L+  QL TG+ HQIRVHM  IGHP+ GD  Y  +
  S:    25 FDQFSRSQIQHWIEDGHVLVNGKQVKPKYKLLVGDHVQII-----PEEPQKIDLAPEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPLGRSLKDRKKQGVVVD-----GRHAVTHFNVLERFKNYTLVACQLETGRTHQIRVHMKYIGHPLAGDPLYGPR 255
>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 = 280, Expect = 3.6e-23, Identities = 83/255 (32%), Positives = 127/255 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN------KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I KE  N++ K        ELS S+ +++IK G + VN K     Y ++E D +   L      +E  L +      L++IYED ++ VVNKP+G++  P       TL N +   +Y  KD       +   + HR+DK T+GL + AKN K    L      +   + Y+ + +G        +        E  I   D++ K        K  +T++ V+E+  +  L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:     4 IIKEAGNRLDKSL--ADLTELSRSQANEAIKAGTVLVNGKLAKAKYVVKEGDVITYVL-----PEEEVLEYKAEDIPLDIIYEDADVAVVNKPQGIVVHPSAGHTSGTLVNAL---MYHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVI--------EAPIGRSDKDRKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR 250
>gi|148256356|ref|YP_001240941.1| ribosomal large subunit pseudouridine synthase C [Bradyrhizobium sp. BTAi1] >gi|146408529|gb|ABQ37035.1| ribosomal large subunit pseudouridine synthase C [Bradyrhizobium sp. BTAi1] (458 aa)
Score = 280, Expect = 3.9e-23, Identities = 73/254 (28%), Positives = 134/254 (52%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILNV----IYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE--EKQIMEIDRE-NKFNKEIITKYRVIEQKKD-MALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + +  +E N  +  F+   F  LS S I + ++ G+++V+ K+     +L+E  +++I  L+L   K+   L+  E K + ++    +YED +++V+NKP GL  Q         +   I + L   +D    +  L HR+D+ T+G  + AK +   T L   + + +  K Y  L  G  K K   +  ++  +E  +  IM +    ++     +T Y V+E   + +A + ++ +TG+ HQ+R HMA IGHP++GD KY
  S:   135 VVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVDGKRADSKDRLEEGQTVRIPPLKLDAPKERAGLSEAERKTLESLKAMTLYEDDDVLVLNKPVGLAVQGGSG-----MTRHIDQMLEVMRDAKGQKPRLVHRIDRETSGCLLIAKTRFAATHLTGAFRSRSARKIYWALVAGVPKPKQGRISTYLAKDEGEDDTIMRVAAHGDEGASHAVTYYAVVEASANKLAWVSLKPVTGRTHQLRAHMAHIGHPIVGDPKY 392
>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 = 280, Expect = 3.9e-23, Identities = 70/237 (29%), Positives = 130/237 (54%)
  Q:    24 KELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++ S S++   +K G ++V+ +    NYK+   +  +I +R   I + ++L  L     L+V+YED ++IV+NKP+G++  P       TL N +  +  +    N ++   + HR+DK T+GL + AKN      L      +   + Y+ L +G+   +  T++  +  ++ ++Q M +  +N  +K  +T +RV+E+ +   ++E +L TG+ HQIRVHM  IG P+ GD KY  +
  S:    26 QDWSRSQVQDWLKAGHVEVDGRIVKPNYKMSGTE--EILVR---IPEAVELEVLPEDIPLDVVYEDSDVIVINKPKGMVVHPAAGHVSGTLVNALLHHCQDLSGINGVKRPGIVHRIDKDTSGLLMVAKNDLAHESLAQQLKDKTTERLYIALVHGEIPHELGTIEAPVGRDKNDRQRMTVTDKN--SKAAVTHFRVLERYEGFTVVECKLETGRTHQIRVHMRYIGFPLAGDPKYGPR 257
>gi|85715100|ref|ZP_01046084.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A] >gi|85698015|gb|EAQ35888.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A] (380 aa)
Score = 279, Expect = 4.2e-23, Identities = 80/265 (30%), Positives = 135/265 (50%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILN-----VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFL--NEEKQIMEIDRE-NKFNKEIITKYRVIE-QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           + +  +E N  +  F+   F  LS S I + ++ G+++VN ++     ++ E D ++I  LRL   K  + L+  E K I +     V++ED +++V+NKP GL  Q         L+  I   L   +D       L HRLD+ T G  + A+ +   T L   +   +  K Y  L  G  K K   +  ++    NEE+ IM +    ++     +T Y V+E   + +A + ++ +TG+ HQ+R HMA +GH ++GD KY  K N  +Q P
  S:    57 VAVTADEANMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGRRADSKDRVSEGDKVRIPPLRLDTPKAAVGLSDAETK-IRDELRKMVLFEDADVMVLNKPAGLAVQGGSG-----LSRHIDGMLETMRDAKGQRPRLVHRLDRETAGCLLIARTRFAATALTGAFRHRSARKIYWALVAGVPKPKQGRISTYLAKEENEEESIMRVAAHGDEGASHAVTYYAVVETSAQKLAWVSLKPVTGRTHQLRAHMAHVGHAIIGDPKYFNKEN--WQLP 323
>gi|168266249|ref|ZP_02688214.1| hypothetical protein LmonFSL_11664 [Listeria monocytogenes FSL J2-071] (302 aa)
Score = 279, Expect = 4.4e-23, Identities = 80/271 (29%), Positives = 134/271 (49%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           +E  ++++ + + KS      S I   +K+GDI VN +    NYK+Q  D +        +++  +L  L     L++ +EDK+++VVNKP G++  P       TL N +  +  +    N  +   + HR+DK T+GL + AKN      L      +   + Y+ L +G    +  T++  I    E++Q M + R+ K   E  T + V+E+     L+  +L TG+ HQIRVH+  IGHP+ GD KY  K         L + K+ F+
  S:    14 RERVDKVIAEMMGKS-----RSAIQLMLKSGDITVNGELAKPNYKVQVGDEIHY-----EVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIEAPIGRAKEDRQKMAVVRDGK---EARTHFEVLERLPGYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPKNTIKGNGQFLHAAKLGFD 273
>gi|78213965|ref|YP_382744.1| ribosomal large subunit pseudouridine synthase D [Synechococcus sp. CC9605] >gi|78198424|gb|ABB36189.1| Pseudouridine synthase, RluD [Synechococcus sp. CC9605] (333 aa)
Score = 279, Expect = 4.9e-23, Identities = 81/256 (31%), Positives = 131/256 (51%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S ++I K I  G ++VN K       L++ D +Q+++   P  + L   +L+ +P+ L+V++ED ++IV+NKP GL   P    K  TL N +   L+   D       L   + HRLDK TTG  V AK+Q+ L  L         S+ Y  + +G     S T+   I  +  + K+   +  EN   +   T + ++E+  D +LL  +L TG+ HQIRVH A + HPV+GD  Y++      + P    + ++   D
  S:    49 EQSRARIQKFIDAGYVRVNGKTGKAKTPLRQGDEVQLWM---PPPEPLP--YLKPEPMDLDVLFEDDHLIVLNKPAGLTVHPAPGNKDGTLVNGL---LHHCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVRLQVQIQKRIASREYFAVVHGVPGGDSGTIVGAIGRHPADRKKYAVVSSEN--GRYACTHWTLVERLGDYSLLRFKLDTGRTHQIRVHCAHMNHPVVGDPTYSRCRKLPIELPGQALHAVQLGLD 301
>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 = 279, Expect = 5.1e-23, Identities = 73/236 (30%), Positives = 129/236 (54%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTEL-NNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +LS S  ++ IK+G I VN +     Y ++E D +   L    +     + ++     L ++Y+D+++ V+NKP+G++  P       TL N +  ++ +    N  L   + HR+DK T+GL + AKN +    L + L + +++ KY+  + +G        ++  I  +E+      DR+ +      K  +T+++V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:    23 DLSRSLANEQIKDGRILVNGQAKKAKYAVKEGDVISYELPEPEV-----VEYVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYW-AIVHGNLPNDRGVIEAPIGRSEK------DRKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR 252
>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 = 279, Expect = 5.2e-23, Identities = 91/256 (35%), Positives = 139/256 (54%)
  Q:     7 KKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL----EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDREN----KFNKEIITKYRVIE--QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN 262
           K E E + L  F+++++ + S S I K +K G + VN ++    + KL+E + + + +   P  + L +   E  PI N+IYED++I VV KP GL+  P       TL N +   LY  KD + +       + HRLDK T G+ V AKN      L   +      K+Y  L  G  KK      D+  ++       +DR+     K  KE +T+Y V++  +K ++ LL++++ TG+ HQIRVH ASIGHPVLGD  Y  K +
  S:    10 KVEGEEERLDKFLARAYPDFSRSYIKKLVKEGLVYVNGEEVRKPSRKLREGERVILHV---PEPEPLDVK-PENIPI-NIIYEDEDIAVVEKPCGLVVHPSPGYTSGTLVNAL---LYHIKDLSSIGGVERPGIVHRLDKETAGVMVIAKNNTAHRNLVRQFQERKTEKFYKVLVKGLVKK------DYGAIDTPIARHPVDRKRFWVRKEGKEALTEYWVLKRYEKYEITLLKVKIHTGRTHQIRVHFASIGHPVLGDRTYGFKSS 262
>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 = 278, Expect = 5.5e-23, Identities = 82/257 (31%), Positives = 141/257 (54%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN 262
           +  EEE + +  ++SK  K+LS S I K I N  + VN +    ++K+   D +++ +   P  ++  +  +E    L++IYEDK+I+V+NK  GL+  P      +TL N +  Y       + +    + HRLDK T+G+ V AKN  +  +L   +      KYY  L  G+   K   +   I  +  +++ M + R+N  +K+ +T ++V+E  +D + +E++L TG+ HQIRVH + +G PV+GD+ Y KK N
  S:    10 VSSEEEGKRIDKYLSKLNKDLSRSYIQKLIDNDKVLVNGESVKRSFKVNRGDHIRLII---PPPEDSGIKPVEMD--LDIIYEDKDILVLNKNAGLVVHPAPGNHENTLVNALIAYCDNLSTISGVNRPGIVHRLDKDTSGVMVIAKNDISHRKLVEQFKQRKTKKYYRTLLKGELPYKEGKIDAPIGRDPHDRKKMAVTRKN--SKKAVTYFKVLEFFRDHSYVEVELKTGRTHQIRVHFSYMGFPVVGDSIYGKKRN 261
>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 = 278, Expect = 5.6e-23, Identities = 74/229 (32%), Positives = 125/229 (54%)
  Q:    29 SKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIME---IDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +KI ++ K+G+I VN K    NYK++ ND +++     P +     N L  + I ++++YED +++VVNKP G++  P       TL N +  Y ++   KN  E   L HR+DK T+GL V AK ++ +T L   +  +   + Y  L +G  ++   T++  I  + + ++        +    K  +T Y+V+E+   + L+  QL TG+ HQIRVHM  IGH +  D +Y
  S:    47 NKIQQAAKDGNIFVNGKPVKSNYKVKGNDVIKVLFAHPPYE-----NLLVGEDIPIDIVYEDDDLLVVNKPAGMVVHPGHGNYSGTLINAL-IYHFDNLPKNSNERPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSERIYYALVWGNVEEDEGTVEGNIGRHPKNRLQNTVFFGEDADKGKPAVTHYKVLERLGYVTLVSCQLETGRTHQIRVHMKHIGHTLFNDERY 274
>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 = 278, Expect = 5.8e-23, Identities = 81/276 (29%), Positives = 143/276 (51%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQ-KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           I+I +  E   + L   +S+   +L+ S I+K  K     +N K +  N K +E D + +      + +  +L  L  +  L+++YED+++I++NKP+G++  P       TL N +  +  +        L   + HR+DK TTG+ +  KN      +       ++++ Y  + YG  K++  T+   I  + ++++ M I  + K     +T Y+V+++ KK    +E QL TG+ HQIRVHMASI HP+LGD  Y  KK  +  +  CL +  + F
  S:     5 IEIKVTSEMAGKRLDVVLSEQCSDLTRSYINKLCKEERAALNGKTSKGNKKCKEGDVITL-----QVPEPTELEILPEEMNLDIVYEDQDVILINKPKGMVVHPAAGHYSGTLVNGLMAHCKDDLSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQSIAKQLYDHSITRKYHAIVYGNIKEEEGTVNAPIGRSLKDRKKMGIVMDGK---HAVTHYKVLKRLKKGFTYIECQLETGRTHQIRVHMASIKHPLLGDDVYGPKKSKYTLEGQCLHAKVLGF 277
>gi|113954535|ref|YP_731894.1| 23S RNA-specific pseudouridylate synthase [Synechococcus sp. CC9311] >gi|113881886|gb|ABI46844.1| 23S RNA-specific pseudouridylate synthase [Synechococcus sp. CC9311] (295 aa)
Score = 278, Expect = 5.9e-23, Identities = 82/256 (32%), Positives = 133/256 (51%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF---LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S S+I K I  G ++VN K       L+  D +Q+++   P  + L   +L+ +P+ L+V++ED+++IV+NKP GL   P    K  TL N +   L+  +D       L   + HRLDK TTG  V AK+Q+ L  L         S+ YL + +G  + +S T+   I    ++ +K  +  D   ++ +   T + + E+  D +LL  +L TG+ HQIRVH A I H V+GD  Y++      + P    +  +   D
  S:    13 EQSRSRIQKFIDAGYVRVNGKTGKAKTPLRNGDQVQLWM---PPPEPLP--YLKPEPMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGL---LHHCQDLPGISGKLRPGVVHRLDKDTTGCIVVAKSQEALVRLQAQIQQRIASREYLAVVHGVPQGESGTIIGAIGRHPVDRKKYAVVSDDSGRYAR---THWTLQERLGDYSLLRFKLDTGRTHQIRVHCAHINHAVVGDITYSRCRKLPVELPGQALHAFQLGLD 265
>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 = 278, Expect = 6.2e-23, Identities = 89/276 (32%), Positives = 145/276 (52%)
  Q:     2 IQIFIKKEEENQILKDFISKSFK-ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN----YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQ-KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN-FGFQFPCLTSYKIKF 277
           I++ +  E     L  F+++  + ELS S I K I+ G + VN      +YK++  + + + L   P  +EL +   E    L+++YED++++VVNK  G++  P +     TL N +   LY  ++ +     L   + HRLDK T+GL V AKN      L      +   + Y  + +G  K K   +   I  +  ++Q M +    K  +   T Y+V+E+  K   L++ +LLTG+ HQIRVH + +GHPVLGD KY  + N FG +   L + K+ F
  S:     5 IKVVVNSEYSGLRLDKFLAEQEELELSRSFIKKLIEEGKVTVNGLHRKASYKVRGGEIIAVLL---PPPRELSVKPEEIP--LDIVYEDEDLVVVNKKAGMVVHPAEGNWDGTLVNAL---LYHCQNLSGIGGVLRPGIVHRLDKDTSGLLVVAKNDLAHQSLAEQIKEKKAVREYWTIVHGYLKNKEGIIDLPIGRHPRDRQKMAVVSNGKTAQ---TVYKVLEEFNKGFTLIQAKLLTGRTHQIRVHFSYLGHPVLGDPKYGHQNNPFGVKRQMLHAIKLSF 277
>gi|91200050|emb|CAJ73092.1| similar to ribosomal large subunit pseudouridine synthase D [Candidatus Kuenenia stuttgartiensis] (335 aa)
Score = 277, Expect = 7.1e-23, Identities = 80/258 (31%), Positives = 134/258 (51%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           + + IK+  E++ +  FIS  F +LS + I K +K G I VN      +Y +++ D +   +   P+ +E K+   E  P LN+IYED  ++++NKP  ++  P       TL N +  Y       N  L+A + HRLD+ T+G+ +  K+    + +   +    V K Y  +  G+    S+ +   I  +  ++Q M + R+    K   + Y VIE+ +   L++I   TG+ HQIRVHM +IGHPV+ D  Y+K
  S:    15 VTLEIKRVGESKRIDRFISSRFPDLSRTYIQKLVKEGAIVVNGNVVKSSYFIKKGDVISATV---PVPEETKIT-PEDIP-LNIIYEDDYLMLINKPYDMVVHPAGGHPSGTLVNAVTFYCQNLSQINGPLKAGIVHRLDRDTSGVMLVIKSDAVHSHIAMQFEKRLVKKEYFAVVEGEVAFDSNEINMPIGRHRVDRQKMAVRRDT--GKNATSVYEVIERFRGYTLVKIMPKTGRTHQIRVHMQAIGHPVVADEMYSK 267
>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 = 277, Expect = 7.1e-23, Identities = 75/275 (27%), Positives = 138/275 (50%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIME---IDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           ++ +  E   Q +   ++    E S S + + + +G + +N K     + K+   D L++ +R  P ++ +   F      L V+YED++++V+NKP GL+  P       TL N +     ++K +    A + HRLDK T+GL V A+N+ T+  L  +     VS+ YL L + ++  +     D     + +  +    +D      K+  T + +++     +L+   L TG+ HQIRVHMAS+GHP++ DT Y  +   G +   L ++++ F
  S:    44 ELTVAAEHHGQRVDKVLALGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRVEMR--PTQQSMA--FQPEAMDLQVVYEDEDLLVINKPAGLVVHPAPGNWTGTLLNGL--LARDEKARQVPRAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQYLALAHKQWGSRKRREVDAPIGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDGDAAHSLVRCTLHTGRTHQIRVHMASLGHPLIADTLYGGQPEGGLERQALHAFRLAF 316
>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 = 277, Expect = 7.2e-23, Identities = 78/269 (28%), Positives = 141/269 (52%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY--NKKGNFGFQFPCLTSYKIKF 277
           +E+ + L  +++    + S S     I+ G + VN + +  NYKL+  D +++ +   P  +EL++   +    L+++YED+++IVVNKP G++  P       TL N +  +  +    N +    + HR+DK T+GL + AK+ K    L +    +   + Y  L  G    +  T+   I  + +++Q M +  EN   ++ +T ++VIE+      +  +L TG+ HQIRVHM  IG+P++GD KY   KK +F  +   L +  + F
  S:     9 DEQGKRLDKWLTDQSDDWSRSLTQSWIQEGYVTVNDETSKANYKLKIGDVVRVKV---PEVEELEITAEDLD--LDIVYEDQDVIVVNKPAGMVVHPAPGHPSGTLVNGLMYHCQDLSGINGVARPGIVHRIDKDTSGLLMVAKHDKAHESLVDQLKNKTTIRQYEALVVGTIPHEKGTVDAPIGRDPQDRQKMTVTEENA--RDAVTHFQVIERMNGYTHVLCELETGRTHQIRVHMKYIGYPIVGDPKYGPRKKHDFSIEGQALHARTLGF 274
>gi|88802386|ref|ZP_01117913.1| ribosomal large subunit pseudouridine synthase D [Polaribacter irgensii 23-P] >gi|88781244|gb|EAR12422.1| ribosomal large subunit pseudouridine synthase D [Polaribacter irgensii 23-P] (346 aa)
Score = 277, Expect = 7.2e-23, Identities = 73/250 (29%), Positives = 128/250 (51%)
  Q:    12 NQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           ++ L +FI  + +    SK+ ++ K G++ VN      N+K++ ND ++I L   P +     + L A+ I L++IYED  +IVVNKP G++  P       TL N +  ++      +     L HR+DK T+GL V AK +  +  L+  +      + Y  L +G   +    ++  I  + + ++ M +  +  F K  ++ Y+V+E+   + L+E +L TG+ HQIR H   IGH +  D +Y   G
  S:    32 DKFLMNFIENATR----SKLQQAAKAGNVLVNEISVKSNHKVKPNDVVRIVLAYPPAE-----SLLVAEDIPLDIIYEDDTVIVVNKPAGMVVHPGHGNYSGTLVNGLIHHIENLPTNSNERPGLVHRIDKDTSGLLVVAKTEFAMANLSRQFFERTTERLYYALVWGNVAEDEGRIEGNIGRSLKNRLQMAVFPDGDFGKHAVSHYKVLERLTYVTLVECKLETGRTHQIRAHFKHIGHTLFNDERYGGDG 274
>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 = 277, Expect = 7.4e-23, Identities = 79/257 (30%), Positives = 135/257 (52%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYK 274
           F+    +  + +KI ++ +NG I VN      NYK++  D +++ L   P  ++L    L  + I L+++YED  ++V+NKP G++  P       TL N +  Y +E    N  E   L HR+DK TTGL V AK +  +  L+  +  +   + Y+ L +G  ++   T++  I  ++  ++ M +   ++  K  +T Y+V+E+   + L+  QL TG+ HQIRVHM  IGH +  D +Y   G+   +    T YK
  S:    34 FLMNMIENTTRNKIQQAAENGSILVNDVAVKSNYKVKAGDVVRLVLA-HPTYEQL----LTPENIPLDIVYEDDQLLVINKPAGMVVHPGHGNYSGTLVNALA-YHFENLPMNSSERPGLVHRIDKDTTGLLVVAKTELAMAYLSKQFAEKTSEREYVALVWGNIEEDEGTVEGNIGRHDTNRMRMAVHESDEKGKPAVTHYKVLERFGYVTLVSCQLETGRTHQIRVHMKHIGHTLFNDERYG--GDSILKGTTFTKYK 285
>gi|27366288|ref|NP_761816.1| ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus CMCP6] >gi|34395774|sp|Q8D8G1|RLUC_VIBVU Ribosomal large subunit pseudouridine synthase C (rRNA-uridine isomerase C) (rRNA pseudouridylate synthase C) >gi|27362489|gb|AAO11343.1|AE016807_62 Ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus CMCP6] (315 aa)
Score = 277, Expect = 7.6e-23, Identities = 82/295 (27%), Positives = 138/295 (46%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKF 300
           I ++   Q + +F+    K++  S I + ++ G+++VN K+    YKL   D     +R+ P+  E K         LN        +IYED +++V+NKP G         K       I+     + +  +LE  L HR+D+ T+G+ + AK +  L  L   +  + V KYY  L  G++K     +   +  NE   I+ ++   K ++   T+++VIE+     L++   +TG+ HQIRVH    GHP+  D +Y  +                  FD     H LN+L L   NI+F
  S:    13 IDEDMAGQRIDNFLRNQLKDVPKSMIYRIVRKGEVRVNKKRVKAEYKLAAGD----VVRIPPVTLEKKDPETAPSTKLNKVAELQDLIIYEDDHLLVLNKPSGTAVHGGSGLKFGA----IEALRALRPEARFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYFALVMGEWKNSCKVVNAPLLKNEVNSIVRVNPNGKPSE---TRFKVIEKFPQATLVQASPITGRTHQIRVHTQYSGHPIAWDDRYGDR-----------------RFDAYTAQHGLNRLFLHAANIRF 285
>gi|146341534|ref|YP_001206582.1| putative ribosomal large subunit pseudouridine synthase RluC-like (23S RNA pseudouridylate synthase) (RNA-uridine isomerase) [Bradyrhizobium sp. ORS278] >gi|146194340|emb|CAL78364.1| putative ribosomal large subunit pseudouridine synthase RluC-like (23S RNA pseudouridylate synthase) (RNA-uridine isomerase) [Bradyrhizobium sp. ORS278] (458 aa)
Score = 277, Expect = 7.6e-23, Identities = 74/254 (29%), Positives = 133/254 (52%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILNV----IYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE--EKQIMEIDRE-NKFNKEIITKYRVIEQKKD-MALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + +  +E N  +  F+   F  LS S I + ++ G+++V+ K+     +L+E  S++I  L+L   K+   L+  E K + ++    +YED +++V+NKP GL  Q         +   I + L   +D    +  L HR+D+ T+G  + AK +   T L   +   +  K Y  L  G  K K   +  ++  +E  +  IM +    ++     +T Y V+E   + +A + ++ +TG+ HQ+R HMA IGHP++GD KY
  S:   135 VVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVDGKRADSKDRLEEGQSVRIPPLKLDAPKERAGLSEGERKTLDSLKAMTLYEDDDVLVLNKPAGLAVQGGSG-----MTRHIDQMLEVMRDAKGQKPRLVHRIDRETSGCLLIAKTRFAATHLTGAFRHRSARKVYWALVAGVPKPKQGRISTYLAKDEGEDDTIMRVAAHGDEGASHAVTYYAVVEASANKLAWVSLKPVTGRTHQLRAHMAHIGHPIVGDPKY 392
>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 = 277, Expect = 7.8e-23, Identities = 80/276 (28%), Positives = 142/276 (51%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           +++ + + EE   L   +++   +L+ + I + ++   + +N K    N K +  DS  + LR+ P  + L L   E  P L+++YED +++VVNKP+G++  P       TL N +  +           +   + HR+DK T+GL + AKN      L       +  + Y  +  G+ K++S  +   I  +  +++ M +  +N  +KE +T +RVI +      + ++L TG+ HQIRVHMA +GHPV GD  Y  +K + G +  CL +  I F
  S:     5 VELVLSEREEGIRLDKVLAERLPDLTRTAIQRLLEEEQVLINGKPAAKNRKGRAGDS--VALRI-PDPEPLCLQ-AENVP-LDIVYEDDDLLVVNKPQGMVVHPAPGNYQGTLVNALLAHCGNSLSGINGVIRPGIVHRIDKDTSGLLMVAKNDFAHQGLARQIKEHSFRREYEAVVAGRMKQESGVVNAPIGRHPIDRKKMAVTEKN--SKEAVTYFRVIAEYPGYTHIRLRLETGRTHQIRVHMAYLGHPVAGDPAYGPRKPDLGLKGQCLHARLIGF 277
>gi|169349798|ref|ZP_02866736.1| hypothetical protein CLOSPI_00536 [Clostridium spiroforme DSM 1552] >gi|169293366|gb|EDS75499.1| hypothetical protein CLOSPI_00536 [Clostridium spiroforme DSM 1552] (278 aa)
Score = 277, Expect = 8.5e-23, Identities = 77/180 (42%), Positives = 110/180 (61%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN 262
           L +IYEDK +IV+NKP GL+     NEK  T  + + +YL  K  K   +  + HRLDK T+G+ + AKN++   +L N WN     + YL +  G+ K+KS T+K++  L+E K  M     NK  K  IT YRV+++ K  +L+EI L TG+K+QIRVHM S+GH ++GD KY    N
  S:    66 LEIIYEDKELIVINKPSGLLSISGGNEKEKTAYHLVGEYLKNKNKK--AKVFVIHRLDKDTSGVLMFAKNEEIKNKLQNNWNKIVYKRGYLAIIEGRLKEKSGTIKNY--LDESKTQMVYITNNKKGKLAITNYRVLKETKYNSLVEIFLDTGRKNQIRVHMQSLGHSIIGDKKYGATTN 241
>gi|119897309|ref|YP_932522.1| pseudouridylate synthase [Azoarcus sp. BH72] >gi|119669722|emb|CAL93635.1| pseudouridylate synthase [Azoarcus sp. BH72] (324 aa)
Score = 276, Expect = 8.9e-23, Identities = 75/246 (30%), Positives = 125/246 (50%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           L   +++ F E S S++   +K+G I+++  +    +K+   + L +   L P+ ++L     EA P L+V+YED +I+V++KP GL+  P       TL N +  +           A + HRLDK TTGL V AK  +  T+L        V+++Y  L YG      +   D      ++  M +       +  +T+Y V ++   + L+E +L TG+ HQIRVHMA +GHP++GD  Y  +
  S:    33 LDQVLARLFPEHSRSRLQAWLKDGLIRLDGMERQAKHKVHGGEEL-VVAGLPPLPEQLAFE-PEAIP-LDVVYEDASILVIDKPAGLVVHPGSGNWSGTLLNALLHH--APALAGLPRAGIVHRLDKDTTGLMVVAKTLEAQTDLVRQLQQRTVARHYYALVYGDIASDGEIDADIDRHPVQRTRMAV---VPGGRPALTRYAVRQRLHGLTLVECRLQTGRTHQIRVHMAHLGHPLVGDPVYGPR 270
>gi|153002938|ref|YP_001377263.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5] >gi|152026511|gb|ABS24279.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5] (339 aa)
Score = 276, Expect = 9.6e-23, Identities = 79/263 (30%), Positives = 134/263 (50%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKP-------ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEA-VSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           M+   I ++   Q L   + K+ +++ LS + K  +   I+VN  +      +   D + I        +E  L   E +P          V++ED +++ V+KP GL   P       TL    + +L    D      + +  HRLD+ T+G+ + AKN+KT+  L  L+   A V K YL L  GK  +++ T+   + L E +Q          N +E +T+++V+   K+ +LL + + TG+ HQIR H+ ++GHPVLGD +Y   G+F
  S:     1 MLTFTISEDAAGQRLDKLVRKALRDVPLSHVYKMFRTRKIRVNGGRGKAEQLVAAGDVVVI-----RGDEERLLARQEPEPGARAGAVTFGVLHEDADVLAVDKPAGLAAHPGTGISGATLVEMARAHLGTPADLPPTEFKPSPAHRLDRDTSGVVLVAKNRKTMVRLTELFTDGADVKKTYLALVKGKMPREAGTID--LPLAEHEQTARSKAARGVNLQEALTRWKVVSAMKEASLLAVTIETGRTHQIRRHLEAVGHPVLGDRRY---GDF 264
>gi|54308380|ref|YP_129400.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium profundum SS9] >gi|46912808|emb|CAG19598.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium profundum SS9] (307 aa)
Score = 276, Expect = 9.6e-23, Identities = 90/297 (30%), Positives = 146/297 (49%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQ---IFL----RLKPIKKEL-KLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKF 300
           I I  +   Q + +F+    K +  S I + ++ G+++VN K+    YKLQ+ D ++   IF+       PI  +L K+  LE+     VIYED +++V+NKP G         K       I+     + D  YLE  L HR+D+ T+G+ + AK +  L +L   +  + V KYY  L  G++K  S  +   +  NE   I+ ++   K +    T+++V+E+ +   L++   +TG+ HQIRVH    GHP+  D +Y          P   +Y  K           LN+L L   NIKF
  S:     4 IDITDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLIRVPPIFMPEQENQAPISTKLSKVAELES----CVIYEDDHLLVLNKPSGTAVHGGSGLKFGA----IEALRALRPDARYLE--LVHRIDRDTSGILLVAKKRSALRKLQEQFREKTVKKYYFALVMGEWKASSKKVTAPLLKNEVNSIVRVNPNGKASD---TRFKVLERFEHATLVQASPVTGRTHQIRVHCQYEGHPIAWDDRYGD--------PRFDAYTKKTG---------LNRLFLHAANIKF 278
>gi|170789030|gb|EDT30074.1| pseudouridine synthase, RluD [Oligotropha carboxidovorans OM5] (412 aa)
Score = 276, Expect = 9.9e-23, Identities = 81/265 (30%), Positives = 134/265 (50%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKL---NFLEA-KPILN-----VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFL--NEEKQIMEIDRE-NKFNKEIITKYRVIE-QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           + +  +E N  +  F+   F  LS S I + ++ G+++VN K+     +L E D++    R+ P+K +      N  EA   +L+     V++ED +++V+NKP GL  Q         L   +   L   +D       L HRLD+ T+G  + AK +   + L   +   +  K Y  L  G  K K   +  ++    NEE  IM I    ++     +T Y V+E   + +A + ++ +TG+ HQ+R HMA IGH ++GD KY  K N  +Q P
  S:    89 VVVTADENNMRVDRFLEAHFPGLSFSHIQRIVRKGELRVNGKRADSKDRLNEGDNV----RIPPLKLDAPKTGGNLSEAGSKVLDELRKMVLFEDADVMVLNKPAGLAVQGGSG-----LTRHVDGMLEVMRDAKGQRPRLVHRLDRETSGCLLIAKTRFAASTLTGSFRHRSARKIYWALVAGVPKPKQGRISTYLAKEENEEDSIMRIAAHGDEGAAHAVTYYAVVEASAQKLAWVSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNKEN--WQLP 355
>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 = 276, Expect = 1.0e-22, Identities = 76/255 (29%), Positives = 126/255 (49%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++ + + +E   +  ++       S ++I KS + G +  N+K    +YK++  D + I +     + E+     E  P LN++YEDK +++VNKP GL+  P       TL N I  ++ +  D   N     L HR+DK T+GL V AK     T L   +  +   + Y  L +G  ++   T+   I  N + ++      +   K  +T YRV+E+   + L+E  L TG+ HQIRVHM  IGH +  D +Y
  S:    32 RVVVDRGQEMMRVDKYLFDRLTNASRNRIQKSAEAGFVMANNKPVKSSYKVKPMDVITIMMDRPRYENEV---IPEDIP-LNIVYEDKYLMIVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRRYRALVWGIVEQDEGTIIGNIGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGHVLFNDERY 284
>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 = 276, Expect = 1.0e-22, Identities = 81/243 (33%), Positives = 127/243 (52%)
  Q:    35 IKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQ--KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           IK G + ++      NY+L+  D +++     P   E      E  P L +I++D +I V+NKP GL+  P +     TL N +   LY  KD       L   + HR+DK T+GL V AKN +    L        V + YL + +G    ++  ++  I  + +++Q M +    K     IT +RV+ +  ++  +LL  +L TG+ HQIRVH+A IGHPV GD KY  +K  FG     L ++K++F
  S:    69 IKEGLVTLDGGPLKANYRLRPGDVIEV----APPAPEAVEILPEDIP-LEIIFQDADIAVINKPAGLVVHPAEGHWSGTLVNAL---LYHIKDLSGINGELRPGIVHRIDKDTSGLLVVAKNDRAHIHLTEQVKDHRVRREYLAVVHGVIGAETGRVEAPIGRDPKDRQRMAVIAGGK---SAITHFRVLARYPEQGFSLLHCRLETGRTHQIRVHLAHIGHPVAGDPKYGPRKAAFGLTGQALHAWKLEF 308
>gi|146300375|ref|YP_001194966.1| RluA family pseudouridine synthase [Flavobacterium johnsoniae UW101] >gi|146154793|gb|ABQ05647.1| ribosomal large subunit pseudouridine synthase D [Flavobacterium johnsoniae UW101] (347 aa)
Score = 276, Expect = 1.1e-22, Identities = 71/246 (28%), Positives = 122/246 (49%)
  Q:    29 SKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYK 274
           +KI  +  +G+I VN      NYK++  D + I L   P +  +    L     LN++YED  ++++NK  G++  P       TL N +  +       +     L HR+DK T+GL V AK +  +T L   +  +   + Y+ L +G    +S T++  +  + +++  M +  + +  K  IT Y+V+E+   + L+  +L TG+ HQIR HM  IGHP+  D +Y   G+   +    T YK
  S:    46 NKIQNAATDGNIFVNDIPVKSNYKVKPFDVITIMLSHPPFENHI----LPEDIPLNIVYEDDALLLINKEPGMVVHPGHGNYTGTLVNALAHHFDNLPMNSSERPGLVHRIDKDTSGLLVVAKTEAAMTHLAKQFEAKTTEREYIALVWGNVAAESGTIEGNLARHLKDRMQMAVFADPEIGKPAITHYKVLERFGYVTLISCKLETGRTHQIRAHMKHIGHPLFNDERYG--GHLILKGTTFTKYK 286
>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 = 276, Expect = 1.1e-22, Identities = 76/255 (29%), Positives = 124/255 (48%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++ + K +E   +  ++       S ++I K+   G +  N K    +YK++  D + + +     + E+     E  P L+++YEDK ++VVNKP GL+  P       TL N I  ++ +  D   N     L HR+DK T+GL V AK     T L N +  +   + Y  L +G  ++   T+   I  N   ++      +   K  +T YRV+E+   + L+E  L TG+ HQIRVHM  IGH +  D +Y
  S:    31 RVVVDKGQEMVRVDKYLFDRLTNSSRNRIQKAADAGFVMANGKAVKSSYKVKPMDVITVMMDRPRYENEV---IPEDIP-LDIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRRYRALVWGNVEQDEGTVVGNIGRNPRDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGHILFNDERY 283
>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 = 276, Expect = 1.1e-22, Identities = 73/256 (28%), Positives = 135/256 (52%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-----LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDREN-----KFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I++ + +  E + L  +I+++ + L+ + + + +++G I VN      + KL+  + L+I +   P+         EA P      L ++YED++++VVNK  G++  P       TL N +  +  +       L   + HR+DK T+G+ V AKN  +   L+  +   ++ + Y+ + YG  K  S  L+  I  +       +DR+      +  K  +T +RVI +   M L+ ++L TG+ HQIRVH++  GHP++GD  Y
  S:     4 IELTVPENTEAERLDSYIARTVETLTRAAVQRLMESGMITVNGMPPKPSLKLKGGEQLKIAVP-PPV---------EAGPAPENIPLEILYEDRDLVVVNKGAGMVVHPGAGNSGGTLVNALLGHCTDLSGIGGELRPGIVHRIDKDTSGILVVAKNDASHLALSEQFREHSIKRIYIAIVYGSPKTDSGRLESIIGRHP------VDRKRMSGKARHGKHAVTHWRVIGRYPGMCLIRLRLETGRTHQIRVHLSEAGHPLVGDEVY 254
>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 = 275, Expect = 1.2e-22, Identities = 77/266 (28%), Positives = 137/266 (51%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT---WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           + +++ EE +  +  ++++   +LS S+I + I+ G ++VN K  T    N K+ +  +L++     P  + L+L   +A+ I L+++YED  ++++NKP GL+  P       TL N +  +         ++   + HRLDK TTG    AK       +     T+   + YL + YG  K  S  +   I  + ++++ M I    +  +  IT +++ E+  +  L+  QL TG+ HQIRVH A IGHP++GD  Y    + G   P
  S:     4 EFYLEVEENSARIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVGDRITLEV-----PEAQPLEL---QAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHSHGTLVNALLAHCPHLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQTKTARREYLGVVYGAPKTSSGKVDLPIGRHPQDRKKMAIVPVEEGGRSAITHWQIQERLGNFTLIHFQLETGRTHQIRVHSAKIGHPIVGDPVYGSGRSVGVNLP 267
>gi|51246876|ref|YP_066760.1| pseudouridine synthase [Desulfotalea psychrophila LSv54] >gi|50877913|emb|CAG37753.1| related to pseudouridine synthase [Desulfotalea psychrophila LSv54] (235 aa)
Score = 275, Expect = 1.2e-22, Identities = 73/201 (36%), Positives = 111/201 (55%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNH 283
           L +++EDK+IIVV KP GL+      EK  T +  +  Y+ +   K+     + HRLD+ T+GL + AK+++    L   W  E   K+YL +  GK K+K  T+  ++  N+  ++       K  K   T Y+VI++ K+++L++I LLTG+KHQIRVH A  GHPV GD KY   G  G +   L +  I F    +H
  S:    19 LPILHEDKDIIVVVKPTGLLTIGTDREKSRTAHYLLNDYVRKGNPKSSNRVYVVHRLDQDTSGLLIFAKSEEAKKFLQKDW--ENTEKHYLAIVCGKLKEKEGTISSYLTENKAYKVYSTPDSTK-GKLSKTAYKVIKEGKEVSLIDIHLLTGRKHQIRVHFAENGHPVAGDKKYG-TGTSGLKRLALHARSISFTHPYSH 215
>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 = 275, Expect = 1.2e-22, Identities = 85/260 (32%), Positives = 143/260 (55%)
  Q:     1 MIQIFIKKEEENQILK--DFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           M +  IK +E+++ L+   ++S  FK+ S S I   I+  ++KVN K    NYKL++ D ++I +       E ++  +EA+ I ++++YED+++IVVNK +G++  P       TL N +   LY  KD       +   + HR+DK T+G+ V AKN     +L+      ++ + Y  L  G+ K    T+   +   ++ ++     E+   K  +T Y V+E+     L++  L TG+ HQIRVHMASIG P++GD  Y  K
  S:     1 MEKTLIKVDEQDEGLRIDKYLSNIFKDKSRSFIQGLIEKENVKVNSKTLKSNYKLKKADEIEIMI------PEPEILSVEAENIPIDIVYEDEDVIVVNKAQGMVVHPAPGNYNGTLVNAL---LYHCKDLSSINGVIRPGIVHRIDKDTSGILVIAKNDDAHNKLSEQLKDHSMKREYYALIEGRLKNNDGTIDKPLGRCKKDRLKIGIIED--GKRAVTHYEVVERYNGYTLVKCVLETGRTHQIRVHMASIGFPLVGDPLYGFK 256
>gi|116072001|ref|ZP_01469269.1| Pseudouridine synthase, RluD [Synechococcus sp. BL107] >gi|116065624|gb|EAU71382.1| Pseudouridine synthase, RluD [Synechococcus sp. BL107] (339 aa)
Score = 275, Expect = 1.2e-22, Identities = 80/256 (31%), Positives = 132/256 (51%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF---LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S ++I K I  G ++VN K+      L+E D +Q+++   P  + L   +L  +P+ L+V++ED++IIV+NK  GL   P    K  TL N +   L+   D       L   + HRLDK T+G  V AK+Q+ L +L         S+ Y  + +G     S T+   +    ++ +K  +  D   ++ +   T + ++E+  D +LL  +L TG+ HQIRVH A I HPV+GD  Y++        P    + ++   D
  S:    52 EQSRARIQKFIDAGYVRVNGKQGKAKTPLREGDQVQLWM---PPPEPLP--YLRPQPMDLDVLFEDEHIIVLNKSAGLTVHPAPGNKDGTLVNGL---LHHCPDLPGISGKLRPGIVHRLDKDTSGCIVVAKSQEALVKLQVQIQKRVASREYFAVVHGVPNGDSGTIIGAVGRHPVDRKKYAVVSDESGRYAR---THWFLVERFGDYSLLRFKLDTGRTHQIRVHCAHINHPVVGDPTYSRCRKLPVDLPGQALHAVQLGLD 304
>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 = 275, Expect = 1.3e-22, Identities = 78/263 (29%), Positives = 133/263 (50%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           L  F++ +   LS ++I   IK G + +N      + +L+  D++ +     P+  E     +  +  L+V++ED ++IV+NKP GL+  P       T+ N +  +              + HRLDK T+G  V AKN      L   +    V+K YL L  GK+ +KS  ++  I  +  +++ M +   +K  +   T YRV+ +     L+E  L TG+ HQIRVH+  +GHP+LGD  Y ++G+F  Q   L ++++ F
  S:    17 LDQFLASAAAGLSRARIQDLIKEGHVTLNGGVAKASARLRAGDAVTLH-EPPPVPTET----VAEEIALDVLFEDDDLIVINKPAGLVVHPAAGNWSGTVVNALLHHCQTLSGIGGEQRPGIVHRLDKDTSGCLVVAKNDAAHQSLAKQFAGREVTKIYLALAAGKWARKSGVIEAPIGRHPVQRKKMTVLPADK-GRAAKTGYRVLLELPVGTLVECTLHTGRTHQIRVHLKHLGHPILGDEVYGRRGDFARQM--LHAWRLGF 273
>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 = 275, Expect = 1.3e-22, Identities = 78/247 (31%), Positives = 131/247 (53%)
  Q:    18 FISKSFKELSLSKISKSIKNGDIKVNHKKTT---WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFG 264
           F+S+   +LS S+I + I+ G++++N K  T    N KL +  +L+I     P  + L+L   E  P L+++YED  ++++NKP GL+  P       TL N +  +         ++   + HRLDK TTG    AK +     L      +   + YL + YG  K +S T+   I  + ++++ M I    +  +  +T ++V+E+  +  L+  QL TG+ HQIRVH A IGHP++GD  Y+   + G
  S:    54 FLSQELPDLSRSRIQQLIEQGNVQLNDKVCTSKKINVKLGDRITLEI-----PEAQPLEL-LAEDIP-LDILYEDDQLLILNKPAGLVVHPAPGHPDGTLVNALLAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTEVAHHHLQAQLKAKTARREYLGVVYGAPKVESGTIDLPIGRHPQDRKKMAIMPIEQGGRSAVTHWQVLERLGNFTLIRFQLETGRTHQIRVHSAKIGHPIVGDPIYSSGHSVG 298
>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 = 275, Expect = 1.4e-22, Identities = 82/265 (30%), Positives = 136/265 (51%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFPCLTSY 273
           E+  Q +   + +   E S ++I   IK   +KVN +    NYK + ND + +       K+ ++ +       L++ YED ++ +V KP+G++  P       TL N +   +Y+ K+       +   + HR+DK T+GL + AKN      L +    + V++ Y+ L +GK      T+   I  N+ ++Q M++  + K   E +T + V+E      L+E QL TG+ HQIRVHM  IG+P++GD KY  K            G  GF+ P    Y
  S:    12 EDTGQRIDKLLPEYHSEWSRTQIQDWIKASLVKVNDQVIKSNYKTKMNDHIVV-----TEKETVEADIQPENLNLDIYYEDDDVAIVYKPKGMVVHPSAGHYTGTLVNGL---MYQMKNLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVDQLVNKTVTRKYVALVHGKIPHDYGTVDAPIGRNKNDRQSMDVVDDGK---EAVTHFNVLEHFNKYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLDIGGQALHAGIIGFEHPVTHEY 282
>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 = 275, Expect = 1.4e-22, Identities = 88/276 (31%), Positives = 137/276 (49%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKE-LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQL-LTGKKHQIRVHMASIGHPVLGDTKYNKKGN---FGFQFPCLTSYKIKF 277
           + I +   E    L  F+ +   E +S + I ++IKNG++ VN      +YK++  D   I     P   E+     E  P L++IYED++I+V+NK  G+I  P  +    T+ N +   LY  KD       L   + HRLDK T+G+ V AKN      L   +      K Y+CL  G  K+K   ++  I  N   ++      +++ K  +T Y+V+ +  D+A L      TG+ HQIRVHM  IGHP++GD  Y +      FG +   L +  + F
  S:     1 MDIQVTSRENGWRLDKFVMEKTPEWISRTFIQRAIKNGEVLVNGTSKKPSYKVKSGD---IITLNAPEAPEIPEILPEDIP-LDIIYEDRDILVINKQPGIITHPIPSHTSGTIVNGV---LYHCKDLQGIGGVLRPGIVHRLDKDTSGVMVIAKNDLAHQSLTKQFKDRLTEKLYICLVKGVPKRKEGDIEINIARNPVLRVKMTVTNSEYGKPALTHYKVVREFGDIAALVFAYPKTGRTHQIRVHMKYIGHPLMGDEVYGRAKEDEIFGIKRQMLHALSLSF 278
>gi|119492077|ref|ZP_01623530.1| Pseudouridine synthase, RluD [Lyngbya sp. PCC 8106] >gi|119453287|gb|EAW34452.1| Pseudouridine synthase, RluD [Lyngbya sp. PCC 8106] (319 aa)
Score = 275, Expect = 1.5e-22, Identities = 81/269 (30%), Positives = 138/269 (51%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKK-TTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI--FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP--CLTSYKIKF 277
           E +N  L  ++S+S + LS S+I   I  G + VN K   +    L+  D +++ +   P  + L+L  ++    L+++YED+++I++NK  GL+  P      DTL N +  +         +E   + HRLDK TTG  V AK   +L  L      +   + YL + YG  K    T++  I   L + K++  +  E +  +  IT +++ E+  + +L+   L TG+ HQIRVH   IGHP++GD  Y+   + G       L ++K+K 
  S:    20 EPQNYRLDRWLSESLETLSRSRIQTLISQGHVTVNQKVCVSKKLTLKRGDHIEVKI---PPNEPLELEAVDIP--LDILYEDEHLIIINKQAGLVVHPSAGHVNDTLVNALLAHCDTLAGIGGVERPGIVHRLDKDTTGAIVVAKTDFSLQSLQQQIKNKTAQRQYLGVVYGSHKADFGTIEQPIGRHLADRKKMAVVTIE-RGGRNAITHWQIQERLGNYSLILFTLETGRTHQIRVHSNFIGHPIVGDLDYSSGRSVGVNLSGQALHAWKLKL 288
>gi|149192304|ref|ZP_01870513.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio shilonii AK1] >gi|148833857|gb|EDL50885.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio shilonii AK1] (315 aa)
Score = 275, Expect = 1.5e-22, Identities = 80/284 (28%), Positives = 136/284 (47%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLN 289
           I  +   Q + +F+    K +  S + + ++ G+++VN K+    YKLQ  DS+    R+ P+  E K         LN        +IYED +++++NKP G+        K       I+     +    +LE  L HR+D+ T+G+ + AK +  L  L   +  + V KYY  L  GK+K     +K  +  NE   I+ ++   K ++   T+++V+E  +   L++   +TG+ HQIRVH    GHP+  D +Y  +           +Y  K   D+  FLH  N
  S:    13 IDDDMAGQRIDNFLRNQLKNIPKSVVYRIVRKGEVRVNKKRVKAEYKLQAGDSV----RIPPVTIEEKQEEAPISTKLNKVAELESQIIYEDDHMLILNKPSGIAVHGGSGLKFGA----IEALRALRPQARFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYFALVMGKWKPSCRVVKAPLLKNEVNSIVRVNPNGKPSE---TRFKVLESFEQATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRR--------FDAYTAKVGLDR-LFLHAAN 282
>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 = 274, Expect = 1.6e-22, Identities = 77/238 (32%), Positives = 126/238 (52%)
  Q:    23 FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKT-LTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
             ELS S  ++ IK+G + VN +     Y +QE D +   +    +     L ++     L ++Y+D+++ VVNKP+G++  P       TL N +   +Y  KD       L   + HR+DK T+GL + AKN    L     L + +++ KY+  + +G        ++  I  +E+      DR+ +      K  +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:    19 LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVTYHVPEPEV-----LEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL---MYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYW-AIVHGNLPNDRGVIEAPIGRSEK------DRKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR 250
>gi|138894182|ref|YP_001124635.1| ribosomal large subunit pseudouridine synthase D [Geobacillus thermodenitrificans NG80-2] >gi|196250721|ref|ZP_03149409.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16] >gi|134265695|gb|ABO65890.1| Ribosomal large subunit pseudouridine synthase D [Geobacillus thermodenitrificans NG80-2] >gi|196209800|gb|EDY04571.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16] (299 aa)
Score = 274, Expect = 1.6e-22, Identities = 67/224 (29%), Positives = 117/224 (52%)
  Q:    40 IKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           +K+N +  +W   L+E D LQ++      + E  L   E +  L+V++ED++++++NK  G+   P + E+  TL N +  YL  +      +    HRLD+ T+G  + AK+      L+ +     + + Y+ L +G+   KS T+   I    ++      R +K     +T YRV+E     +L+E+ L TG+ HQIRVH+A +GHP++GD  Y  +  F
  S:    46 VKLNGQAVSWQTTLRERDRLQLY----AYEPEPSLIIPEYRE-LSVLWEDEHLLILNKEAGIDIHPSEPEQTGTLANAVAFYL--QSQAILTKVRHIHRLDRDTSGTILFAKHPLAGATLDRMLAHRTIKRTYVALVHGRLSPKSGTISAPI--GRDRHHPTRRRVSKTGARAVTHYRVLETFPSASLVELNLDTGRTHQIRVHLAHLGHPLVGDMLYGGQPTF 260
>gi|37679452|ref|NP_934061.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio vulnificus YJ016] >gi|37198196|dbj|BAC94032.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio vulnificus YJ016] (315 aa)
Score = 274, Expect = 1.6e-22, Identities = 81/295 (27%), Positives = 138/295 (46%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKF 300
           I ++   Q + +F+    K++  S I + ++ G+++VN K+    YKL   D     +R+ P+  E K         LN        +IYED +++V+NKP G         K       I+     + +  +LE  L HR+D+ T+G+ + AK +  L  L   +  + V KYY  L  G+++     +   +  NE   I+ ++   K ++   T+++VIE+     L++   +TG+ HQIRVH    GHP+  D +Y  +                  FD     H LN+L L   NI+F
  S:    13 IDEDMAGQRIDNFLRNQLKDVPKSMIYRIVRKGEVRVNKKRVKAEYKLAAGD----IVRIPPVTLEKKDPETAPSTKLNKVAELQDLIIYEDDHLLVLNKPSGTAVHGGSGLKFGA----IEALRALRPEARFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYFALVMGEWENSCKVVNAPLLKNEVNSIVRVNPNGKPSE---TRFKVIEKFPQATLVQASPITGRTHQIRVHTQYSGHPIAWDDRYGDR-----------------RFDAYTAQHGLNRLFLHAANIRF 285
>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 = 274, Expect = 1.6e-22, Identities = 77/238 (32%), Positives = 126/238 (52%)
  Q:    23 FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKT-LTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
             ELS S  ++ IK+G + VN +     Y +QE D +   +    +     L ++     L ++Y+D+++ VVNKP+G++  P       TL N +   +Y  KD       L   + HR+DK T+GL + AKN    L     L + +++ KY+  + +G        ++  I  +E+      DR+ +      K  +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:    19 LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVTYHVPEPEV-----LEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL---MYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYW-AIVHGNLPNDRGVIEAPIGRSEK------DRKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR 250
>gi|145953052|ref|ZP_01802060.1| hypothetical protein CdifQ_04003029 [Clostridium difficile QCD-32g58] (429 aa)
Score = 274, Expect = 1.6e-22, Identities = 87/264 (32%), Positives = 140/264 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGD-------TKYNKKGN------FGFQFPCLTSYKIKFN 278
           L  ++++   ++S S I K IK+G +KVN+K     Y ++E D++ I      I +   L  L     ++++YED +++++NKP+ ++  P      +TL N I   LY  KDK       +   + HR+DK T+GL + AKN      L        +++ Y  +CYG  K+   T+   I  N + ++ M + ++ K     IT + V+E+      +  +L TG+ HQIRVH  SI HP+LGD       TK+  KG        GF  P    Y I+FN
  S:   144 LDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKAKYLVKEEDNIVI-----EIPEPKVLEVLPQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGI---LYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNPKDRLKMAVVKDGK---NAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLLGDFVYGPKETKFKLKGQTLHAKKLGFIHPTTKEY-IEFN 414
>gi|82702194|ref|YP_411760.1| pseudouridine synthase, RluD [Nitrosospira multiformis ATCC 25196] >gi|82410259|gb|ABB74368.1| ribosomal large subunit pseudouridine synthase C [Nitrosospira multiformis ATCC 25196] (328 aa)
Score = 274, Expect = 1.7e-22, Identities = 78/252 (30%), Positives = 134/252 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLE---AKP---ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDT----LKDFIFLNEEKQI-MEIDR-ENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I +E + Q + +F+ K  K +  S + + +++G +++N K+   +Y LQ  D     +R+ P++   K        +KP      V++ED  +I VNKP G+                I++   +  D  +LE  L HRLD+ T+G+ + AKN+  L EL+       V K+YL L  G+++    +    L+ ++    E+++ +E D  E K      T + + E  +  +LLE +L TG+ HQIRVH+A +G P+ GD KY
  S:     5 IGEESKGQRIDNFLIKRLKNVPKSHVYRLLRSGQVRINSKRAPPDYHLQSGD----IVRIPPVRTVEKSALPPKKLSKPGFIAFQVLFEDDALIAVNKPPGVAVHGGSGISFGV----IEQLRAQHPDWRFLE--LAHRLDRETSGVLLLAKNRAALVELHRQLRMGEVEKHYLTLVKGRWRNGRQSVRLSLRKYLTPGGERRVAVEKDADEKKGGMSAHTVFILRESWQSFSLLEAELKTGRTHQIRVHLAYLGFPIAGDDKY 258
>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 = 274, Expect = 1.7e-22, Identities = 82/252 (32%), Positives = 132/252 (52%)
  Q:     9 EEENQILKD-FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           EEE  I  D F++   + +S + I     +G I +N K     YKL   D +++ +      K      +EA+ I LN++YED+++IVVNKP+G++  P       TL N +   LY   D       +   + HR+DK T+G+ V AKN     +L   +   ++ + Y  +  G+FKK+  T+   +  +   ++     ++   K  +T Y V++     +L++  L TG+ HQIRVHMA IGHP+LGDT Y  K
  S:    12 EEEKGIRADKFLALKIEGVSRNFIQGLFDDGKILINGKAEKGKYKLSVGDCVEVEIPEPEELK------VEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNAL---LYHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVVKD--GKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLK 258
>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 = 274, Expect = 1.7e-22, Identities = 77/236 (32%), Positives = 126/236 (53%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKT-LTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ELS S  ++ IK+G + VN +     Y +QE D +   +    +     L ++     L ++Y+D+++ VVNKP+G++  P       TL N +   +Y  KD       L   + HR+DK T+GL + AKN    L     L + +++ KY+  + +G        ++  I  +E+      DR+ +      K  +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:    21 ELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVTYHVPEPEV-----LEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL---MYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYW-AIVHGNLPNDRGVIEAPIGRSEK------DRKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR 250
>gi|84394338|ref|ZP_00993060.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio splendidus 12B01] >gi|84375031|gb|EAP91956.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio splendidus 12B01] (314 aa)
Score = 274, Expect = 1.8e-22, Identities = 82/295 (27%), Positives = 139/295 (47%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKF 300
           I ++   Q + +F+    K +  S I + ++ G+++VN K+    YKL+  D     +R+ P+  E K         LN        +IYED +++++NKP G         K       I+     + D  +LE  L HR+D+ T+G+ + AK +  L  L   +  + V KYY  L  G++K     +   +  NE   I+ ++   K ++   T+++V+E+ +D  L++   +TG+ HQIRVH    GHP+  D +Y  +                  FD       LN+L L   NIKF
  S:    13 IDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKLKAGD----LVRIPPVTIEEKTEENVPSTKLNKVSELEQCIIYEDDHMLILNKPSGTAVHGGSGLKFGA----IEALRALRPDSRFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYFALVMGEWKNSCKVVNAPLLKNEVNSIVRVNPNGKASE---TRFKVLEKFQDATLVQASPITGRTHQIRVHAQYTGHPIAWDDRYGDR-----------------RFDAYTGKVGLNRLFLHAANIKF 285
>gi|167757067|ref|ZP_02429194.1| hypothetical protein CLORAM_02616 [Clostridium ramosum DSM 1402] >gi|167703242|gb|EDS17821.1| hypothetical protein CLORAM_02616 [Clostridium ramosum DSM 1402] (279 aa)
Score = 274, Expect = 1.8e-22, Identities = 74/180 (41%), Positives = 109/180 (60%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN 262
           L++IYED+ +IV+NKP GL+     NEK  T  + + +YL + K+KN     + HRLDK T+G+ + AKN+    +L N WN     + YL +  GK KKK  T+K+   L+E K  M     N   K  IT Y+V+++ +  +L+E+ L TG+K+QIRVHM S+GH ++GD KY    N
  S:    66 LDIIYEDRELIVINKPAGLLSMAGGNEKEKTAYHLVGEYL-KSKNKN-ARVFIVHRLDKETSGVLLFAKNEIIKNKLQNNWNDIVYKRGYLAIIEGKLKKKHGTIKNH--LDESKTQMVYIANNGKGKLAITNYKVLKESRYNSLIEVFLETGRKNQIRVHMQSLGHSIVGDKKYGATTN 241
>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 = 274, Expect = 1.9e-22, Identities = 86/292 (29%), Positives = 150/292 (51%)
  Q:     5 FIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVK 296
            ++K+ EN  ++D++ K     S   I  +     + VN K    +Y++ E D +++      + K    N    K  LN++YED +IIV+NKP  +I  P KN +  TL+N +  Y  EK +   +   L +RLD  T+GL + AKNQ +   L      +   K Y+ +  G       T+   I+  EE+ I     +    +E IT + V+E+ K+   +++ L TG+ HQIRVH++SIG+P++GD+ Y ++     +   L ++K++F   ++  +     +N+EVK
  S:     9 LVEKKYENFKIRDYL-KQVHGFSTRLIRGAAFGERLFVNGKTVRLSYRVLEGDKIEV-----DVNKPESQNVDPEKMDLNIVYEDSDIIVLNKPANMIVHPTKNYQHGTLSNGLLYYFREKGENCIVR--LVNRLDMDTSGLVLVAKNQFSHMALARDMKLDTFKKEYIAVVRGNLSSLKGTIDKPIYKEEEEPIRRTIDDR--GQESITHFEVVERYKNADKVKLVLETGRTHQIRVHLSSIGNPIIGDSLYGEESEL-IKRQALHAFKLQFPHPRDGRI-----VNIEVK 284
>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 = 274, Expect = 1.9e-22, Identities = 84/266 (31%), Positives = 136/266 (51%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFPCLTSY 273
           KE+    +   + +   + S ++I   IK G +  N K    NYK++ ND + +       K+ ++ + L     L++ YED ++ VV KP+G++  P      +TL N +   +Y+ K+       +   + HR+D  T+GL + AKN     EL      ++V + Y+ L +G       T+   I  N+ ++Q M +  + K   E +T + V+E  KD  L+E QL TG+ HQIRVHM  IG P++GD KY  K            G  GF+ P    Y
  S:    11 KEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLNDHIVV-----TEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGL---MYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRELVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGRNKNDRQSMAVVDDGK---EAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTGEY 282
>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 = 274, Expect = 1.9e-22, Identities = 92/297 (30%), Positives = 146/297 (49%)
  Q:     5 FIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNY-LEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF-NFDKNHFLHYLNKLNLEVKNIKFK 301
            I + E N  L  FISK F+E S S   K I+  ++ VN+     NYKL+  D ++I      IK++ K+N       LN+IYED+++IV++KP+G++  P       TL N +  +       N  +   + HR+DK T+G+ V AKN      L+      ++ + Y+ L  G  K     +   +  N + +I      N   K  +T Y V+ +     L++  L TG+ HQIRVHMA I HP++GD  Y  +K  F      L + K+ F +     ++ + ++L    K I FK
  S:     7 LINESEVNSRLDVFISKCFEEKSRSYAQKLIEEKNVFVNNSSKKSNYKLKIGDYVEI-----KIKEDEKINIKPEDIKLNIIYEDEDVIVIDKPQGMVVHPGAGNYSGTLVNGLLYHCDSLSSINGDVRPGIVHRIDKDTSGVLVVAKNDSAHIILSEQLKEHSMKREYIALVEGIIKNDEGIIDAPLGRNPKDRIKRAVVRN--GKSAVTHYNVLRRFNKNTLVKCILETGRTHQIRVHMAHINHPLVGDPMYGFRKQRFKLNGQMLHARKLGFIHPSSKKYMEFQSELPNYYKEILFK 299
>gi|59712354|ref|YP_205130.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114] >gi|59480455|gb|AAW86242.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114] (315 aa)
Score = 274, Expect = 1.9e-22, Identities = 79/265 (29%), Positives = 136/265 (51%)
  Q:    13 QILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIK---------KELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------GNFGFQFPCLTSYKIKF 277
           Q + +F+    K +  S I + ++ G+++VN K+    YKLQE D     +R+ P+K           +KL  + A+    +IYED +++++NKP G         K       I+     + D  +LE  L HR+D+ T+G+ + AK +  L  L   +  + V KYY  L  G++K     +   +  NE   I+ ++   K ++   T+++V+E+ +   L++   +TG+ HQIRVH    GHP+  D +Y  +      G FG     L +  IKF
  S:    20 QRIDNFLLARLKNVPKSMIYRIVRKGEVRVNKKRIKPEYKLQEGD----VVRIPPVKVPESTAPDLPNVKLGKV-AELEHCIIYEDDHVLILNKPSGTAVHGGSGLKFGA----IEALRALRPDARFLE--LVHRIDRDTSGILLVAKKRSALRRLQEQFRNKTVQKYYFALVMGQWKNSCKVVNAPLLKNEVNSIVRVNPNGKPSE---TRFKVLEKFEQATLIQASPITGRTHQIRVHTQYTGHPIGWDDRYGDRRFDAYTGQFGLDRLFLHAANIKF 285
>gi|33866856|ref|NP_898415.1| putative pseudouridylate synthase specific to ribosomal large subunit [Synechococcus sp. WH 8102] >gi|33639457|emb|CAE08841.1| putative pseudouridylate synthase specific to ribosomal large subunit [Synechococcus sp. WH 8102] (331 aa)
Score = 274, Expect = 2.0e-22, Identities = 80/256 (31%), Positives = 126/256 (49%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S ++I K I  G ++VN K       L++ D +Q+++   P  + L   +L+ +P+ L+V++ED ++IV+NKP GL   P    K  TL N +   L+   D       L   + HRLDK TTG  V AK+Q+ L  L         S+ YL + +G     S T+   I  +   +       +   +   T + + E+  D +LL  +L TG+ HQIRVH A I HPV+GD  Y++      + P    +  +   D
  S:    49 EQSRARIQKFIDAGYVRVNGKTGKAKTPLRQGDEVQMWM---PPPEPLP--YLKPEPMALDVLFEDDHLIVINKPAGLTVHPAPGNKDGTLVNGL---LHHCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQQALVRLQGQIQKRIASREYLAVVHGVPGGDSGTIVGAIGRHPADRKKYAVVNDDSGRYACTHWTLQERLGDYSLLRFKLDTGRTHQIRVHCAHINHPVVGDPTYSRCRKLPMELPGQALHAFQLGLD 301
>gi|110803816|ref|YP_699133.1| pseudouridine synthase [Clostridium perfringens SM101] >gi|110684317|gb|ABG87687.1| pseudouridine synthase [Clostridium perfringens SM101] (306 aa)
Score = 273, Expect = 2.0e-22, Identities = 83/252 (32%), Positives = 131/252 (51%)
  Q:     9 EEENQILKD-FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           EEE  I  D F++     +S + I     +G I +N K     YKL   D +++ +      K      +EA+ I LN+IYED+++IVVNKP+G++  P       TL N +   LY   D       +   + HR+DK T+G+ V AKN     +L   +   ++ + Y  +  G+FKK+  T+   +  +   ++     ++   K  +T Y V++     +L++  L TG+ HQIRVHMA IGHP+LGDT Y  K
  S:    12 EEEKGIRADKFLALKIDGVSRNFIQGLFDDGKILINGKAEKGKYKLSVGDCVEVEIPEPEELK------VEAEDIPLNIIYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNAL---LYHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVVKD--GKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLK 258
>gi|150024746|ref|YP_001295572.1| 23S rRNA pseudouridine synthase [Flavobacterium psychrophilum JIP02/86] >gi|149771287|emb|CAL42756.1| Probable 23S rRNA pseudouridine synthase [Flavobacterium psychrophilum JIP02/86] (347 aa)
Score = 273, Expect = 2.0e-22, Identities = 71/246 (28%), Positives = 129/246 (52%)
  Q:    29 SKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYK 274
           +KI ++  +G+I VN+     NYK++  D + I L   P +     N ++ + I L+++YED  ++++NKP GL+  P       TL N +  +       +     L HR+DK TTGL V AK ++ +T L   +  +   + Y+ + +G  +K   T++  +  + +++  M +  + +  K  IT Y+V+E+   + ++  +L TG+ HQIR H+  IGHP+  D +Y   G+   +    T YK
  S:    46 NKIQQAATSGNIFVNNIPVKSNYKVKPFDVVTIMLSHPPFE-----NRVDPEDIPLDIVYEDDALLLINKPAGLVVHPGHGNYTGTLVNALAFHFQNLPLNSSERPGLVHRIDKDTTGLLVIAKTEQAMTHLAKQFENKTSEREYIAIVWGNVQKDEGTIEGNLARHLKDRMQMAVFADPEIGKPAITHYKVLERFGYITVISCKLETGRTHQIRAHLKHIGHPLFNDERYG--GHLILKGTTFTKYK 286
>gi|90413248|ref|ZP_01221243.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium profundum 3TCK] >gi|90325800|gb|EAS42258.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium profundum 3TCK] (314 aa)
Score = 273, Expect = 2.0e-22, Identities = 90/297 (30%), Positives = 147/297 (49%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQ---IFLRLK----PIKKEL-KLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKF 300
           I I  +   Q + +F+    K +  S I + ++ G+++VN K+    YKLQ+ D ++   IFL  +    PI  +L K+  LE+     VIYED +++V+NKP G         K       I+     + D  YLE  L HR+D+ T+G+ + AK +  L +L   +  + V KYY  L  G++K     +   +  NE   I+ +++  K +    T+++V+E+ +   L++   +TG+ HQIRVH    GHP+  D +Y          P   +Y  K           LN+L L   NIKF
  S:    11 IDITDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLIRVPPIFLPEQADQAPISTKLSKVAELES----CVIYEDDHLLVLNKPSGTAVHGGSGLKFGA----IEALRALRPDARYLE--LVHRIDRDTSGILLVAKKRSALRKLQEQFREKTVQKYYFALVMGEWKASCKKVTAPLLKNEVNSIVRVNQNGKASD---TRFKVLERFEHATLVQASPVTGRTHQIRVHCQYEGHPIAWDDRYGD--------PRFDAYTKKTG---------LNRLFLHAANIKF 285
>gi|54294221|ref|YP_126636.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate synthase) (Uracil hydrolyase) [Legionella pneumophila str. Lens] >gi|53754053|emb|CAH15526.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate synthase) (Uracil hydrolyase) [Legionella pneumophila str. Lens] (321 aa)
Score = 273, Expect = 2.0e-22, Identities = 81/261 (31%), Positives = 121/261 (46%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           Q+ + +E  NQ +   +++   E S S I   IK G + +N+       K    D + I +       +  L   E  PI  ++YED  +IVVNKP  L+  P    K  TL N +  +  E +      A + HRLDK TTGL + AKN  + T L        + ++YL L +G           F    + +  M +     F ++ +T Y + +  KD  LL + L+TG+ HQIRVHM  I HPV+GD  Y  +  F
  S:     8 QLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLITINVDYTIDNTDFNLCKPENIPI-QIVYEDSEVIVVNKPASLVVHPGAGNKEHTLVNALLHHCPELQ--LLPRAGIIHRLDKDTTGLLIVAKNLISHTYLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHPKNRLKMAV---TDFGRQAVTHYNINKHYKDFTLLNVSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKF 262
>gi|148977658|ref|ZP_01814234.1| 23S rRNA ribosomal pseudouridine synthase [Vibrionales bacterium SWAT-3] >gi|145963173|gb|EDK28441.1| 23S rRNA ribosomal pseudouridine synthase [Vibrionales bacterium SWAT-3] (314 aa)
Score = 273, Expect = 2.1e-22, Identities = 78/272 (28%), Positives = 136/272 (50%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------GNFGFQFPCLTSYKIKF 277
           I ++   Q + +F+    K +  S I + ++ G+++VN K+    YKL+  D     +R+ P+  E K+        LN        +IYED +++++NKP G         K       I+     + +  +LE  L HR+D+ T+G+ + AK +  L  L   +  + V KYY  L  G++K     +   +  NE   I+ ++   K ++   T+++V+E+ KD  L++   +TG+ HQIRVH    GHP+  D +Y  +      G  G     L +  IKF
  S:    13 IDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKLKAGD----LVRIPPVTIEEKVEENVPSTKLNKVSELEQCIIYEDDHMLILNKPSGTAVHGGSGLKFGA----IEALRALRPEARFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYFALVMGEWKNSCKVVNAPLLKNEVNSIVRVNPNGKASE---TRFKVLEKFKDATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKF 285
>gi|169183561|ref|ZP_02844064.1| pseudouridine synthase, RluA family [Thauera sp. MZ1T] >gi|169009298|gb|EDS56077.1| pseudouridine synthase, RluA family [Thauera sp. MZ1T] (319 aa)
Score = 273, Expect = 2.1e-22, Identities = 77/260 (29%), Positives = 139/260 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEA---KPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLK----DFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           I +    Q + +++ +  K +  S + + +++G+++VN ++    Y+LQE D +    R+ PI+     +   A   KP L V+YED+ ++V++KP G                 I++   ++ +   LE  L HRLD+ T+GL + AK +  LT L+++    +V K YL L  G++      +K     ++    E+++   D E K    I+   R++ + +D +LLE++L TG+ HQIRVH+A +G  + GD KY   G+F  
  S:    16 IDEAAAGQRIDNYLLRIAKGVPKSHVYRILRSGEVRVNGRRVQQTYRLQEGDEV----RIPPIRIAEPTHAAPAPAGKP-LPVVYEDEALLVIDKPSGKAVHGGSGVSYGV----IEQLRVQRPELRMLE--LAHRLDRETSGLLIVAKKRSALTALHDMMREGSVEKRYLTLVPGRWSNPLQHVKVPLHKYLTAEGERRVRVAD-EGKAAHSIV---RLVRRWRDYSLLEVELKTGRTHQIRVHLAHLGFALCGDDKY---GDFAL 264
>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 = 273, Expect = 2.1e-22, Identities = 79/253 (31%), Positives = 130/253 (51%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           K E+  +  D       +LS S  ++ IK G I VN       Y ++E D +   L   P  +E++  ++     L ++Y+D+++ VVNKP+G++  P       TL N +   +Y  KD       L   + HR+DK T+GL + AKN +    L +    +   + Y  + +G        ++  I  +E+      DR+ +      K  +T+++V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:     4 KVEQAGVRLDKAVADLTDLSRSLANEQIKTGKILVNGLVKKAKYTVKEGDVISYEL---PEIEEIE--YVTENIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL---MYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK------DRKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR 250
>gi|56478533|ref|YP_160122.1| ribosomal large subunit pseudouridine synthase C [Azoarcus sp. EbN1] >gi|56314576|emb|CAI09221.1| ribosomal large subunit pseudouridine synthase C [Azoarcus sp. EbN1] (318 aa)
Score = 273, Expect = 2.1e-22, Identities = 76/253 (30%), Positives = 135/253 (53%)
  Q:    13 QILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNF--LEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKD--FIFLNEE-KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           Q + +++ +  K +  S + + +++G+++VN  +    Y+L END +    R+ PI+   K       A   L V++ED+ ++VV+KP G                 I++   ++ D   LE  L HR+D+ T+GL V AK +  LT L+++     V K YL L  G++      +K+  F +L  E ++ + +  + K +  I+   R++ +    +LLE++L TG+ HQIRVH+A +G P+ GD KY   G+F  
  S:    21 QRIDNYLLRICKGVPKSHVYRILRSGEVRVNGGRVAPTYRLAENDEI----RIPPIRLAEKTTSGPAPAGEPLPVVFEDEALLVVDKPSGKAVHGGSGVSFGV----IEQLRSQRPDARLLE--LAHRIDRETSGLLVIAKKRSALTALHDMMREGRVEKRYLTLVPGRWANPLQHIKEPLFKYLTAEGERRVRVSGDGKASHSIV---RLVRRWSRFSLLEVELKTGRTHQIRVHLAHLGFPLCGDDKY---GDFAL 262
>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 = 273, Expect = 2.1e-22, Identities = 81/263 (30%), Positives = 132/263 (50%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI---FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           L   ++  F + + S++ K I +G+IKVN      NYK+   D +         K E+K   LE + I L+++YED ++IVVNKP+G++  P       TL N +  +             + HR+DK T+GL + AKN      L      +  ++ Y+ L +G  K+ S T+   +    ++ +KQ +  D  N      +T + V+++  D  L++  L TG+ HQIRVHM  IGHP++GD  Y  +   G     L + K+ F
  S:    14 LDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDVKKANYKVNLGDEITF------DKPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHSPLSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYVALVHGNIKEDSGTIDAPLGRSKVDRKKQAVVKDGRNA-----VTHFEVLKRYGDYTLVKCVLETGRTHQIRVHMKYIGHPLVGDQLYGPRKTLGNSGQFLHAEKLGF 269
>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 = 273, Expect = 2.2e-22, Identities = 81/290 (27%), Positives = 156/290 (53%)
  Q:     2 IQIFIKKEEENQILKD-FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY--NKKGNFGFQFPCLTSYKIKFNFDK-NHFLHYLNKL 291
           I+ FI  EE+  I  D F+S   ++ S   + K  K G++ +N +K   + KL   + +++ L    +     L+ +     +N++YED+++++V+KP+G++  P       TL N +  ++ +    N  +   + HR+DK T+GL + AKN      L   +   ++++ Y  +C+G   + S T+   I  ++ +++ M + + N  +K  +T + VI++      L++ L TG+ HQIRVH+  I HPV+GD  Y  N + +  F+   L +YK+ F   K N ++ + ++L
  S:     3 IKEFIVTEEKQNIRCDKFLSDKLEDFSRESLKKLFKEGEVFLNDEKVKPSRKLIAGERVKVNLPEPEV-----LDVIAENIPINIVYEDEDVVIVDKPQGMVVHPANGNHSGTLVNALMYHVKDLSSINGVIRPGIVHRIDKDTSGLLIIAKNDNAHNHLAVQFKEHSINRRYKTICHGIIHENSGTIDAPIGRDKIKRKEMCVTQSN--SKRAVTHFDVIKRYDKYTFLDVHLETGRTHQIRVHLKYISHPVIGDKVYGFNSQIDRPFKGQLLHAYKLGFIHPKTNEYMEFNSEL 291
>gi|30249427|ref|NP_841497.1| rluC; ribosomal large subunit pseudouridine synthase C [Nitrosomonas europaea ATCC 19718] >gi|30138790|emb|CAD85367.1| rluC; ribosomal large subunit pseudouridine synthase C [Nitrosomonas europaea ATCC 19718] (343 aa)
Score = 273, Expect = 2.2e-22, Identities = 74/260 (28%), Positives = 139/260 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDT----LKDFIFLNEEKQIMEIDRENKFNK--EIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           I +  E+Q + +F+ +S K +    I + +++G ++VN K+   +Y+LQ  D ++I   ++ +K              N++Y+D +++V++KP G+             +  I++   +  D  +LE  L HRLD+ T+G+ + A+ +++L EL+       V K+YL L  GK+K         L  ++    E+++      N  +K  +  T + + +  +D +LL+ +L TG+ HQIRVH+A +G P+ GD KY   G+FG 
  S:    29 IDETAESQRIDNFLIRSLKGIPRRHIYQLLRSGQVRVNSKRIDASYRLQLGDKVRIPPVIRSVKPVSSQGVYRTDR-FNILYQDDHLLVIDKPAGIAVHGGSG----ISHGVIEQLRGQHPDWKFLE--LVHRLDRETSGILLLARKRQSLLELHRQIREGTVEKHYLTLVRGKWKNSVQNVRLPLNKYLTAAGERRVAVAAGRNDQDKAQQAHTLFTLQKAWEDFSLLDAELKTGRTHQIRVHLAHLGFPIAGDDKY---GDFGL 284
>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 = 273, Expect = 2.3e-22, Identities = 80/252 (31%), Positives = 131/252 (51%)
  Q:     9 EEENQILKD-FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           EEE  I  D F++     +S + I     +G I +N K     YKL   D +++ +      K      +EA+ I LN++YED+++IVVNKP+G++  P       TL N +  +  +    N  +   + HR+DK T+G+ V AKN     +L   +   ++ + Y  +  G+FKK+  T+   +  +   ++     ++   K  +T Y V++     +L++  L TG+ HQIRVHMA IGHP+LGDT Y  K
  S:    12 EEEKGIRADKFLALKIDGVSRNFIQGLFDDGKILINGKAEKGKYKLSVGDCVEVEIPEPEELK------VEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVVKD--GKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLK 258
>gi|83815887|ref|YP_445314.1| ribosomal large subunit pseudouridine synthase D [Salinibacter ruber DSM 13855] >gi|83757281|gb|ABC45394.1| ribosomal large subunit pseudouridine synthase D [Salinibacter ruber DSM 13855] (349 aa)
Score = 273, Expect = 2.3e-22, Identities = 81/264 (30%), Positives = 142/264 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI-FLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKY---------------------------LYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY-NKKGNFGFQ----------------FPCLTSYKIKFN 278
           +  ++++ + E S +KI ++IK G +KVN      +Y ++  D +    +R  P++ E      EA P L+V++E  +++VVNKP G++  P    +  TL + +  +                           L +  D   +   + HRLDK T+GL V AK  +    L   +    V + Y  + +G+F     T++  I  +   +Q M +  E++  K   T Y  +E     +++E +L TG+ HQIRVH  + GHP+LGD KY  ++  +G Q                 P L +Y++ F+
  S:    11 IDKYLTRFYPEASRTKIQRAIKKGHLKVNGTDVKKSYGVEPGDEIVFRLIRKPPMQAEP-----EAIP-LDVVHEGDDLLVVNKPAGMVVHPAPGHRSGTLVHALLHHVDGGEVAADDERDEVSEDEVGLSLVNALPQSPDHPVVRPGIVHRLDKGTSGLLVVAKRGRAHQPLAEQFKAHTVDRRYRAIVWGRFAPSDGTIEGAIGRDPHHRQRMAVVPEDE-GKWARTHYETVETHAHTSVVEFELETGRTHQIRVHARAQGHPLLGDPKYGGQRVRYGTQSGTRRTFYDQLFETLPHPALHAYRLGFD 313
>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 = 273, Expect = 2.4e-22, Identities = 84/266 (31%), Positives = 135/266 (50%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFPCLTSY 273
           KE+    +   + +   + S ++I   IK G +  N K    NYK++ ND + +       K+ ++ + L     L++ YED ++ VV KP+G++  P      +TL N +   +Y+ KD       +   + HR+D  T+GL + AKN      L      ++V + Y+ L +G       T+   I  N+ ++Q M +  + K   E +T + V+E  KD  L+E QL TG+ HQIRVHM  IG P++GD KY  K            G  GF+ P    Y
  S:    11 KEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLNDHIVV-----TEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGL---MYQIKDLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGRNKNDRQSMAVVDDGK---EAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTGEY 282
>gi|50083692|ref|YP_045202.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ADP1] >gi|49529668|emb|CAG67380.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ADP1] (310 aa)
Score = 273, Expect = 2.5e-22, Identities = 81/255 (31%), Positives = 134/255 (52%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELK------LNFLEAKPILN-VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSD----TLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           + + +  Q + +F+    K +  S+I + I+ G ++VN K+     KL   D +    R+ PI+ E K      ++   AK +LN V+YED+ ++VVNKP G+            +     + +     K YLE  L HR+D+ T+GL + +K + TL  L +L     + K Y  L  G+           L  +   N E+++  + +E K +K   T++RV E+ K+  L+    L+G+ HQIRVH  SIGHP++GD KY  +
  S:    15 VDEHQAGQRIDNFLFTRLKGVPKSRIYRLIREGQVRVNKKRIKAESKLSIGDQI----RVAPIRYEQKDESDAPVSDQVAKSLLNRVVYEDEGLLVVNKPSGIAVHGGSGVAYGLI-----EAMRAATGKKYLE--LIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIRKTYAALVKGQVSLDQQLIDAPLLRYELSNGERRV-RVSKEGKPSK---TEWRVAERFKEATLVYASPLSGRTHQIRVHGLSIGHPLVGDDKYGHQ 265
>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 = 273, Expect = 2.5e-22, Identities = 80/252 (31%), Positives = 131/252 (51%)
  Q:     9 EEENQILKD-FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           EEE  I  D F++     +S + I     +G I +N K     YKL   D +++ +      K      +EA+ I LN++YED+++IVVNKP+G++  P       TL N +  +  +    N  +   + HR+DK T+G+ V AKN     +L   +   ++ + Y  +  G+FKK+  T+   +  +   ++     ++   K  +T Y V++     +L++  L TG+ HQIRVHMA IGHP+LGDT Y  K
  S:    12 EEEKGIRADKFLALKIDGVSRNFIQGLFDDGKILINGKAEKGKYKLSVGDCVEVEIPEPEELK------VEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVVKD--GKRAVTHYEVLKVFNSCSLVKCNLETGRTHQIRVHMAFIGHPLLGDTVYGLK 258
>gi|23098304|ref|NP_691770.1| hypothetical protein OB0849 [Oceanobacillus iheyensis HTE831] >gi|22776530|dbj|BAC12805.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831] (303 aa)
Score = 272, Expect = 2.6e-22, Identities = 73/252 (28%), Positives = 134/252 (53%)
  Q:    10 EENQILKDFISKSFKELSLSKISKSIKNGDIKVN-HKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           EE + L  F+ K     S + +   +  G + V+ H +T  N+ L +  +++I      I++++ +        ++++YED +IIV+ K  GL+    + E+  T  +++  Y+ ++   N     + HRLDK T+G+ + AKN++   +L N W      + Y+ L  G+  K+   +  ++  +  ++ M   R     +   T+YRV++     +LLE+QL TG+K+QIRVHM  +GHPV+GD +Y  KG
  S:    21 EETEQLLPFLLKVMDNRSRNSVKSILTRGQVSVDDHIETKHNFMLNKGSTVRILKNKAAIQQDVFVG-------MSIMYEDDDIIVIEKESGLLSIATEKERKHTALHQLMHYVKQQHPAN--RVYVVHRLDKDTSGVMMFAKNERVKRKLQNNWKDIVKERTYVALVEGQVAKEKGYIVSWLKESATRK-MYSSRVKNDGQRAATRYRVLQTNNRYSLLELQLETGRKNQIRVHMEELGHPVVGDKRYGSKG 263
>gi|196258950|ref|ZP_03157483.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822] >gi|196200270|gb|EDX95092.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822] (305 aa)
Score = 272, Expect = 2.6e-22, Identities = 77/263 (29%), Positives = 136/263 (51%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT-WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFG 264
           ++I ++ E+    L  ++++   +LS S++   I+ G++++N K  T    K+Q+ D L +F+   P++    LN    +  L+V+YED+ +I++NKP GL+  P    +  TL N +  +         ++   + HRLDK TTG  V AK       L      +   + YL + YG  K  S T+   I  +  E++ M +    K  +  IT + + E+  +  L+  +L TG+ HQIRVH  ++GHP++GD  Y+   + G
  S:     1 MEITLQVEQGKLRLDVWLAQKIPDLSRSRLQNLIEQGNLRLNGKICTDKKTKVQQGDLLYLFI--PPVEP---LNLQPEEIPLDVLYEDEQLIIINKPAGLVVHPAPGHEKGTLVNALLSHCSNLAGIGGVQRPGIVHRLDKDTTGALVIAKTDYAHQHLQAQLKAKTARREYLGVVYGVPKTGSGTINLPIGRHPIERKKMAVVPLEKGGRVAITHWEIRERLGNYTLIHFRLETGRTHQIRVHSTAMGHPIVGDPVYSSGRSIG 261
>gi|189463385|ref|ZP_03012170.1| hypothetical protein BACCOP_04104 [Bacteroides coprocola DSM 17136] >gi|189429814|gb|EDU98798.1| hypothetical protein BACCOP_04104 [Bacteroides coprocola DSM 17136] (307 aa)
Score = 272, Expect = 2.7e-22, Identities = 74/243 (30%), Positives = 131/243 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKV-NHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           L +F+ K    +S +++   + N  + V N+ +T +NY L+    +QI    +  K E +       P+L ++YED  +IVV K  GL+     ++K  T  + + +Y+  +   N     + HRLD+ T+G+ + AK++KT   L + W+     + Y+ +  G  +K   T++ +  L + K  +     +   K  +T YR I++    +L+E+QL TG+K+QIRVHM S+GHPV+GD +Y
  S:    31 LMEFLMKKMAGISRTRVKALLTNRVVLVDNNIQTLYNYPLKPGMKVQI--SREKNKHEFR------HPMLKILYEDAYLIVVEKKEGLLSVATDHQKEKTAQHILNEYVKRQHRNN--RVFVVHRLDRETSGIMMYAKDEKTQHTLRDNWHDIVRDRRYVSIVMGDMEKDQGTVESW--LTDRKLYVSSSPVDDGGKYSVTHYRTIKRANGYSLVELQLETGRKNQIRVHMQSLGHPVVGDERY 262
>gi|160946974|ref|ZP_02094177.1| hypothetical protein PEPMIC_00936 [Peptostreptococcus micros ATCC 33270] >gi|158447358|gb|EDP24353.1| hypothetical protein PEPMIC_00936 [Peptostreptococcus micros ATCC 33270] (318 aa)
Score = 272, Expect = 2.8e-22, Identities = 94/257 (36%), Positives = 141/257 (54%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKEL--KLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKI-DTLNNRIKKYLYEKKDKN-----YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           M  I +   +  Q +  F+ K     S S I K ++   IKVN KK   NY L END + IF+  + ++K +  K         L++IYED+NIIV+NKP+ L+      E   + L + +  YL EK D N          + +RLD+ T+GL + AKN K L ELN L    ++ KYY  +  GK KK    + + +  +EEK    I   +K  K+ IT+  V +   + +LL+I+L+TG+ HQIR H++S G  ++GD KY
  S:     1 MRDIEVNNNDSGQRIDRFLKKYLNNASTSMIQKFLRTKKIKVNRKKVDSNYILAENDVINIFIYEEELEKLIVSKSKKYSYSKKLDIIYEDENIIVMNKPKNLLSHASSKEDYGNNLVDFMIGYLLEKGDYNPRAEKTFVPAIINRLDRNTSGLVIGAKNSKALRELNRL-KENSIEKYYKTIVSGKVKKNF-VINEKLEKDEEKNKSTI---SKNGKDSITEIYVEKNNDEFSLLKIKLITGRTHQIRSHLSSKGFYIIGDIKY 260
>gi|134045627|ref|YP_001097113.1| RluA family pseudouridine synthase [Methanococcus maripaludis C5] >gi|132663252|gb|ABO34898.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C5] (298 aa)
Score = 272, Expect = 2.8e-22, Identities = 92/297 (30%), Positives = 160/297 (53%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEA-KPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKN 297
           ++++ I  +     L D +   F ELS   I K  K   I VN K  +   KL+EN+++ + +       +  +N ++  K +L VIYED ++++V+KP+ ++  P KN    TL N I  +  +K +    +    +RLD  TTGL + AKN  +  +L    +   + K Y+ +  G    K   ++D I LN++    E+    K +K   TKY+VIE+  ++++LEI+LLTG+ HQIRVH++S G+ ++GDT Y K  +   +   L S+ ++       F+H + K N+E+++
  S:     7 ILKVTIDSKIAGNKLIDVLKDDF-ELSNKMIKKFDKEKKIFVNSKNISLKSKLKENETVSVEI-------DCGINNIDPEKLLLCVIYEDDDLLIVDKPKNMVVHPTKNVLSGTLANAISNH--QKINNQNYKIRFVNRLDMDTTGLLIIAKNSYSHQQLAKQMDEGILEKIYIVVVNGHLDSKEGVIEDSIDLNDDGIKRELSTFGKISK---TKYKVIEEFNNVSVLEIKLLTGRTHQIRVHLSSFGNNIIGDTLYGKTADL-IERQALHSHILR-------FIHPITKENMEIRS 283
>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 = 272, Expect = 2.9e-22, Identities = 80/260 (30%), Positives = 132/260 (50%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFL-RLKPIKKELKLNFLEA--KPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN---EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           M   F    E+ +I K  I+      + S++ K +++G + VN + T  NYK+   D + I +   KP         LEA  +PI L+++YED  +IVV+KP+G++  P       TL N +  +         +   + HR+DK T+GL + AK +K    L+     +   + YL L +G FK+   T+   +  +    ++Q +  D      +  +T ++V+E+ +    ++  L TG+ HQIRVHMA I HPV GD  Y  K
  S:     1 MTSTFTITTEQGRIDK-VITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASGDVIAISIPEAKP---------LEAIPEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRDRKRQAVVAD-----GRHAVTHFQVLERFEHYTFIKCILETGRTHQIRVHMAYIHHPVAGDPLYGPK 252
>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 = 272, Expect = 2.9e-22, Identities = 73/270 (27%), Positives = 135/270 (50%)
  Q:    10 EENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTL-NNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN--FGFQFPCLTSYKIKFNF 279
           +  Q +  ++     + S S+I + IK+  ++VN      +Y L+  D++++     P      LN       L ++YED +++ ++KP G++          TL N  + ++         L   + HRLD++T+G+ + AKN     +L   ++   + K YL L +G  K ++  ++  I  +   +     R  +  +   ++YRV+ +  D  LLE+++ TG+ HQIRVH+ASI HPV+GDT Y        G  F  L +++I+F+ 
  S:     9 DTGQRIDQWLHAHLPDFSRSRIQEWIKSARVRVNGAAVKTSYTLRAADAVEVEPADPP-----PLNATAEDIPLRILYEDADVVAIDKPAGMVVHAGAGVHSGTLVNALLHRFATLSGVGGPLRPGIVHRLDRFTSGVLLVAKNDAAHQKLAAQFSGREIEKVYLALVHGTVKPETGRIERPIARDPVHRARMTARLAE-GRAAWSEYRVLRRFPDFTLLEVRIGTGRTHQIRVHLASIRHPVVGDTLYGAPAQPLLGRYF--LHAHRIRFHL 273
>gi|60682049|ref|YP_212193.1| putative RNA pseudouridylate synthase [Bacteroides fragilis NCTC 9343] >gi|60493483|emb|CAH08269.1| putative RNA pseudouridylate synthase [Bacteroides fragilis NCTC 9343] (305 aa)
Score = 272, Expect = 3.0e-22, Identities = 75/252 (29%), Positives = 134/252 (53%)
  Q:    10 EENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT-WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           +E   L DF++    + S +K+   +    + V++  TT +N+ LQ    +++ +     KKE +       P+L ++YED  IIVV K  GL+    + +K  T  + + +Y+      N +   + HRLD+ T+GL + AK++KT   L + W+     + Y+ +  G+ +K SDT+  +  L +    +     +    + IT YR I++    +L+E++L TG+K+QIRVHM  +GHP++GD +Y   G
  S:    22 KEPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQP--GMKVLISKDKNKKEFR------HPLLKIVYEDAYIIVVEKKEGLLSVGTERQKERTAQHILSEYVGRSGRGNRIY--VVHRLDRDTSGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSW--LTDRTLYVSSSSYDDGGSKSITHYRTIKRANGYSLVELRLETGRKNQIRVHMQDLGHPLIGDGRYGIDG 262
>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 = 272, Expect = 3.0e-22, Identities = 75/246 (30%), Positives = 130/246 (52%)
  Q:    12 NQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-----DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++ L +FI  + +    +KI K+ K+G+I VN      NYK++  D++Q+     P +  L     E  P L+++YED  ++VVNK  G++  P       TL N +  +     + +     L HR+DK T+GL V AK ++ +  L+  +  ++  + Y+ + +G   ++  T++  I  N   ++  I     D EN   K  +T Y+V+E+   + L+  +L TG+ HQIRVHM  IGH +  D +Y
  S:    38 DKYLMNFIENATR----NKIQKAAKSGNIYVNGDTVKQNYKVKGGDTVQVMFEHPPYEYLL---VPEDIP-LDIVYEDDTLLVVNKQAGMVVHPGHGNYSGTLINALVHHFDNLPNNSSDRPGLVHRIDKDTSGLLVVAKTEEAMAHLSKQFFDKSSEREYVAIVWGNLAEEEGTIEGNIGRNPRNRLQNIVFEGDDVEN--GKAAVTHYKVLERLGYVTLVACKLETGRTHQIRVHMKYIGHTLFNDERY 278
>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 = 272, Expect = 3.1e-22, Identities = 80/252 (31%), Positives = 131/252 (51%)
  Q:     9 EEENQILKD-FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           EEE  I  D F++     +S + I     +G I +N K     YKL   D +++ +      K      +EA+ I LN++YED+++IVVNKP+G++  P       TL N +  +  +    N  +   + HR+DK T+G+ V AKN     +L   +   ++ + Y  +  G+FKK+  T+   +  +   ++     ++   K  +T Y V++     +L++  L TG+ HQIRVHMA IGHP+LGDT Y  K
  S:    12 EEEKGIRADKFLALKIDGVSRNFIQGLFDDGKILINGKAEKGKYKLSVGDCVEVEIPEPEELK------VEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVVKD--GKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLK 258
>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 = 272, Expect = 3.1e-22, Identities = 93/281 (33%), Positives = 154/281 (54%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN----LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKFNFDKNH 283
           +  I    +N  L  F++    ELS S+I K I++  + VN+K    NYKL  ND ++        +KE K      K  L+V+YED  + ++NK + +I  P +    DTL N +   +Y  K+ + ++ +    + HRLDK TTGL + AK+  T  +L  +     + K YLC+ +GK  + S T+K+++  N ++++ M +  E K +   I++Y  ++   D +L+++Q+ TG+ HQIRVHM  I HP+LGD  Y  KK    F    L +Y ++F   + H
  S:     4 EFLIDDSNQNTRLDVFLANEV-ELSRSEIQKFIEDKKVLVNYKPQKKNYKLNSNDKIKF-----DYEKEDK-TIRAQKHDLDVVYEDDYLAIINKDKDVIVHPTETIYSDTLVNYL---MYNFKNLSDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKTYLCIVHGKIDE-SGTIKEYMTRNPKDRKKMMVSDEGKLS---ISQYERLDYNDDYSLVKVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKKEKILFDSQVLHAYNLQFIHPQTH 276
>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 = 272, Expect = 3.1e-22, Identities = 75/262 (28%), Positives = 137/262 (52%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL----EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE--EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFG 264
           Q  ++ +E+ Q L  F+    K LS +  ++ I+ G + V+      +Y L+  + + + +  +P   ++    ++    L ++YED++I+ VNKP G++  P      +TL N +   L   KD + +       + HRLDK T+G+ +AAKN      L+       V K+YL L +G  K+ +  + D        +++ M +    K  +E ++ + V E+  D   +++Q+ TG+ HQIRVH+A++ HPV+GDT Y  +   G
  S:     8 QFKVQNKEQGQRLDAFVPVHCKNLSRNACARLIRQGLVTVDKSVKKPSYVLKPGEMVSVTVP-EPETADIVAQDMD----LAILYEDRDIVAVNKPPGMVVHPAPGHSSNTLVNAL---LAHCKDLSGIGGVQRPGIVHRLDKETSGVILAAKNDAAHAGLSEQLAQRRVEKFYLALAHGVIKEDTGVI-DLPLARHPSDRKRMHVSTPAK-GREALSLWTVKERFLDATYVKVQIKTGRTHQIRVHLAALHHPVIGDTVYGGRKKRG 265
>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 = 272, Expect = 3.2e-22, Identities = 78/254 (30%), Positives = 123/254 (48%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY--NKKGNFGFQFP 268
           L   +S    E S ++I   I+   I V+    T   K+   +S+++ +   P       +  EA P L+V+YED  ++V+NKP GL+  P    +  TL N +   + +  +     A + HRLDK T+GL V AK  +  T+L        V + YL L YG+  +          L  +         +   KE +T Y V+E+   + LL  +L TG+ HQIRVHM  +GHP++GDT Y  +++ +    FP
  S:    27 LDQALSALLPEFSRNRIQNWIRARKIVVDDAWGTTKMKVSGGESVRVQVEPDPGATP---DAPEAIP-LDVVYEDSMLLVINKPVGLVVHPGSGNRDGTLLNALLHRVPQVAE--LPRAGIVHRLDKDTSGLLVVAKTLRAHTDLVRQLQARTVKREYLALVYGEVDRGGTVDAP---LARDPHNRTKRTVHSLGKEAVTHYDVVERFPGITLLRCKLETGRTHQIRVHMQHVGHPLVGDTVYSASRRSHLKIPFP 273
>gi|108759922|ref|YP_634049.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622] >gi|108463802|gb|ABF88987.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622] (318 aa)
Score = 272, Expect = 3.3e-22, Identities = 77/265 (29%), Positives = 127/265 (47%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPI-----KKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEI-ITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           MI+  I+ +     L   + K    + +S + K I+   ++VN K+      L E D L I    + +      K            L ++ ED  ++ V+KP G+           TL + ++ YL  K  +N   A+  HRLD+ T+G+ + AK +  +     ++      K YL L  GK  + S  +   + L+E +Q  E       N +  +T+++V++Q  + ALL   + TG+ HQIR H+A+IGHPV GD KY   G+F F
  S:     1 MIEYRIEADTAGMRLDKHLRKRLPNVPVSHLFKMIRTKKVRVNGKRAQPEQLLSEGDVLTIRGDEQQLVGAERPKVDPPPPPVDPSRLVILREDDWLMAVDKPSGMAVHTGSGITGGTLVDYVRAYLGPKAVRNDFAASPAHRLDRETSGVILVAKRRPAMVHFTEVFTHGLSRKRYLTLVKGKMPRDSGVID--LPLSEHQQTAESKARRGVNMQAAVTRWKVVKQSSEAALLSCAIETGRTHQIRRHLAAIGHPVAGDKKY---GDFAF 266
>gi|88800777|ref|ZP_01116334.1| pseudouridine synthase [Reinekea sp. MED297] >gi|88776483|gb|EAR07701.1| pseudouridine synthase [Reinekea sp. MED297] (328 aa)
Score = 272, Expect = 3.3e-22, Identities = 81/235 (34%), Positives = 122/235 (51%)
  Q:    23 FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENK-----------FNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           F + S S+I + IK G + VN K      KL   ++L + + L+  ++       EA+P+ LNV+YED+ IIV++KP GL+  P       T+ N +   LY   +   +  A + HRLDK TTGL V A+     T L       ++ + Y  LC G              +NE      IDR  K             K+ IT YRV ++ ++  L+  +L TG+ HQIRVH++ IG+P++GD  Y
  S:    31 FADYSRSRIQQWIKEGRLTVNGKTLKPRDKLIGGETLTLDVTLESDER------WEAEPVELNVVYEDEQIIVIDKPAGLVVHPGAGTPSGTVLNGL---LYRYPELAAVPRAGIVHRLDKDTTGLMVVARTLTAQTHLAGQLQDRSMGREYYALCMGVMTGGG-------VVNEP-----IDRHPKHRTKMAVAPTGMGKDAITHYRVEQRFRNHTLVRCKLETGRTHQIRVHLSHIGYPLVGDPLY 257
>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 = 272, Expect = 3.3e-22, Identities = 74/243 (30%), Positives = 126/243 (51%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNY---LEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEI-ITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +  F+    +  + S+I   I+   +KVN K T  +YK++  D + I L   P +  L     E  P L+++YED  I++VNK  G++  P       TL N +  Y +E    +    +   L HR+DK T+GL V AK    +T +   +   ++ + Y  +C+G    KS T+K+++  + + + +    EN+ + ++ IT Y+ +     +AL++  L TG+ HQIR HM SIGH +  D  Y
  S:    36 IDKFLMSRIQYATRSRIQYGIEIDSVKVNDKSTKASYKVRPGDVITISLPHPPREDVL---IPEDIP-LDIVYEDDQILIVNKKPGMVVHPAHGNWTGTLVNALA-YHFENLPTHVNGKIRPGLIHRIDKDTSGLLVIAKTDYAMTFMAKQFADHSIERTYYAICWGVPDPKSGTIKNYLGRSTKDRKLVTTYENEEDGKLAITHYKTLAAYHYVALIQCNLETGRTHQIRAHMKSIGHSLFNDMSY 277
>gi|124024488|ref|YP_001018795.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9303] >gi|123964774|gb|ABM79530.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9303] (324 aa)
Score = 271, Expect = 3.4e-22, Identities = 79/256 (30%), Positives = 130/256 (50%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S S I K I+ G ++VN         L++ D +Q+++   P  + L   +L+ + + L+V++ED+++IV+NKP GL   P    +  TL N +   L+   D       L   + HRLDK TTG  V AK+Q+ L +L         S+ YL + +G       T+   I  +  + K+   +  +    +   T + ++E+  D +LL  QL TG+ HQIRVH A IGHP++GD  Y++        P    + ++   D
  S:    40 EQSRSHIQKFIEAGLVRVNGITGRAKTPLRQGDEVQLWM---PPPEPLP--YLQPEAMHLDVLFEDRHLIVINKPAGLTVHPAPGNRNGTLVNGL---LHHCSDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQQQIQKRIASRNYLAVVHGAPTGDQGTIVAAIGRHPVDRKKYAVVTEDG--GRHACTHWTLVERLGDYSLLRFQLDTGRTHQIRVHCAHIGHPIVGDPIYSRCRKLPIDLPGQILHAVQLGLD 292
>gi|29349120|ref|NP_812623.1| ribosomal large subunit pseudouridine synthase D [Bacteroides thetaiotaomicron VPI-5482] >gi|29341027|gb|AAO78817.1| ribosomal large subunit pseudouridine synthase D [Bacteroides thetaiotaomicron VPI-5482] (357 aa)
Score = 271, Expect = 3.5e-22, Identities = 73/231 (31%), Positives = 119/231 (51%)
  Q:    27 SLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE--KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           S ++I K+ ++G +  N K    +YK++  D + + +     + E+     E  P LN++YED  ++VVNKP GL+  P       TL N +  ++ +  + D N     L HR+DK T+GL V AK     T L   +  +   + Y  L +G  ++   T+   I  N +++  M +  +    K  +T YRV+E+   + L+E  L TG+ HQIRVHM  IGH +  D +Y
  S:    55 SRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVMMDRPRYENEI---IPENIP-LNIVYEDPYVMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPEYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRRYRALVWGNVEQDEGTIVGSIARNPKDRMQMAVMSDPSMGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGHVLFNDERY 284
>gi|146296964|ref|YP_001180735.1| RluA family pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM 8903] >gi|145410540|gb|ABP67544.1| pseudouridine synthase, RluA family [Caldicellulosiruptor saccharolyticus DSM 8903] (292 aa)
Score = 271, Expect = 3.6e-22, Identities = 79/274 (28%), Positives = 149/274 (54%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNF 279
           IKK++ N   K+ + K    LS + +SK   NG I+         + + ++ +++  + L+   K++  N +  K  +++++ED+  + VNKP G+   P K    DTL N ++ YL    +   + +++ +RLDK T+G+ V AKN    + +++ +    + K Y+ +  G   KKS  ++  I  + +    EI+ +  +    IT Y V++ K + ++L+++ +TG+ HQ+RVH+ASIG+P++GD  Y    N  F    L +Y +KF+F
  S:     7 IKKDDLNMTYKEILRKKLF-LSSTLLSKLKSNGQIRF----IPPIFSINQHPTVESIIELE--LKDVYSNIVPIKGSIDILFEDQFFLFVNKPSGIPSHPSKGHYFDTLANNVEWYL----NSQGVTSHIINRLDKDTSGIVVFAKNSYFHSIVSSEFEKRTIEKTYIAVVDGILTKKSGFIEKPISRSNDGIKREINEDGDY---AITYYEVVDYKNNYSILKLKPITGRTHQLRVHLASIGYPIVGDVLYGTGKNKNFPL-LLHAYSMKFDF 265
>gi|153808958|ref|ZP_01961626.1| hypothetical protein BACCAC_03259 [Bacteroides caccae ATCC 43185] >gi|149128291|gb|EDM19510.1| hypothetical protein BACCAC_03259 [Bacteroides caccae ATCC 43185] (357 aa)
Score = 271, Expect = 3.7e-22, Identities = 74/231 (32%), Positives = 119/231 (51%)
  Q:    27 SLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE--KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           S ++I K+ ++G +  N K    +YK++  D + + +     + E+     E  P LN++YEDK ++VVNKP GL+  P       TL N +  ++ +    D N     L HR+DK T+GL V AK     T L   +  +   + Y  L +G  ++   T+   I  N +++  M +  +    K  +T YRV+E+   + L+E  L TG+ HQIRVHM  IGH +  D +Y
  S:    55 SRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVVMDRPRYENEI---IPEDIP-LNIVYEDKYVMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDVPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRKYRALVWGTVEQDEGTIVGNIARNPKDRMQMAVMSDPAVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGHVLFNDERY 284
>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 = 271, Expect = 3.8e-22, Identities = 72/235 (30%), Positives = 119/235 (50%)
  Q:    26 LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           LS  + +  IK G + VN ++    Y +Q  D +   L      KE  L +      L++IYED  + ++NKP+G++  P      +T+ N +  ++ +    N  +   + HR+DK T+GL + AK       L      +   + YL + +G        ++  I  +E+      DR+ +      KE +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:    22 LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFEL-----PKEEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSETMVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQALTEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEK------DRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR 250
>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 = 271, Expect = 3.8e-22, Identities = 94/289 (32%), Positives = 157/289 (54%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGN-------------FGFQFPCLTSYKIKFNFD-KNHFLHYLNKL 291
           +  +  EEE   L  ++S    E+S S I K IK+  +KVN K     Y ++E+DS+ I +   P  K L++  +     ++++YED ++++VNKP+ ++  P      +TL N I   LY  KD        +   + HR+DK T+G+ + AKN      L       ++++ Y  +C+G  K+   T+   I  N + ++ M I ++ K     +T + VI++ ++   ++  L TG+ HQIRVH ASIGHP+LGD  Y  K +              GF  P    Y ++FN D  ++F+  LNK+
  S:    10 EFLVLGEEEGDRLDVYLSSQLGEMSRSYIQKIIKDKKVKVNGKIEKAKYAVKEDDSVVIEI---PAPKLLEV--IPQDIPIDIVYEDDDLLIVNKPQDMVVHPAPGNYENTLVNAI---LYHCKDNLSSINGVIRPGIVHRIDKDTSGILMIAKNNNAHNSLAEQLKDHSITREYEFICHGVVKEDKITVDRPIGRNPKDRLKMAIVKDGK---RAVTHFEVIKRYENFTHMKANLETGRTHQIRVHAASIGHPLLGDPIYGPKNSKIKCKGQTLHARKLGFIHPTTKQY-VEFNSDLPDYFVEILNKI 306
>gi|53713831|ref|YP_099823.1| RNA pseudouridylate synthase [Bacteroides fragilis YCH46] >gi|52216696|dbj|BAD49289.1| RNA pseudouridylate synthase [Bacteroides fragilis YCH46] (307 aa)
Score = 271, Expect = 4.0e-22, Identities = 75/252 (29%), Positives = 134/252 (53%)
  Q:    10 EENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT-WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           +E   L DF++    + S +K+   +    + V++  TT +N+ LQ    +++ +     KKE +       P+L ++YED  IIVV K  GL+    + +K  T  + + +Y+      N +   + HRLD+ T+GL + AK++KT   L + W+     + Y+ +  G+ +K SDT+  +  L +    +     +    + IT YR I++    +L+E++L TG+K+QIRVHM  +GHP++GD +Y   G
  S:    24 KEPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQP--GMKVLISKDKNKKEFR------HPLLKIVYEDAYIIVVEKKEGLLSVGTERQKERTAQHILSEYVGRSGRGNRIY--VVHRLDRDTSGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEIEKDSDTVVSW--LTDRTLYVSSSSYDDGGSKSITHYRTIKRANGYSLVELRLETGRKNQIRVHMQDLGHPLIGDGRYGIDG 264
>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 = 271, Expect = 4.0e-22, Identities = 87/284 (30%), Positives = 152/284 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTL-NNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-KGNFGFQFPCLTSYKIKFNFDKN----HFLHYLNKLNLEVKNI 298
           L  ++S++  + + S + K I+ G++ VN  +     YK++  D +++ +   P  K+L L    A+ I + V+YED+++ V+NKPRG++  P      +TL N  + K+       N  +   + HRLDK T+GL + AK  +   +L+    +  + + Y  +C G  K+ S  +   I  +   ++      N   KE +T + V+E+      ++++L TG+ HQIRVHM+ IG+P+LGD+ Y + K  FG Q   L + +I+F         HF   L +  LE+ NI
  S:    10 LDKYLSEALSK-TRSFVQKIIEEGNVWVNQSQVLKPAYKVKSGDIIKVVI---PEPKQLSL---VAQDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKFSGRLSSINGVIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHPVNRLKMAVVPN--GKEAVTYFEVLERFDKYTFIKLRLKTGRTHQIRVHMSYIGYPLLGDSSYGRAKNEFGVQGQVLHAGEIEFVHPITSKVLHFSADLPEYFLEILNI 293
>gi|150390922|ref|YP_001320971.1| RluA family pseudouridine synthase [Alkaliphilus metalliredigens QYMF] >gi|149950784|gb|ABR49312.1| pseudouridine synthase, RluA family [Alkaliphilus metalliredigens QYMF] (308 aa)
Score = 271, Expect = 4.2e-22, Identities = 80/257 (31%), Positives = 133/257 (51%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           MI   ++ E++ Q LK+ + K+  +LS   ++K  K+  I +N +   ++  L E D ++I +       E    F   +   NV+YED ++IV+NK  G++  P K+   DT+ N  + YL  +K          +RLD  T+GL V AKN  T   ++       ++K Y+    G        +   I+ + ++ I  +  +    ++ +TK+ V+E+  D  +LE+ LLTG+ HQIRVHM SIGHP+LGD  Y
  S:    11 MITYEVEAEDDQQPLKETL-KNRLDLSSRLLTKLKKSKRILINGQYAKYHELLSEGDWIKIDM------TEEASQFEPQEIPFNVVYEDIDVIVINKEPGIVSHPTKSHPKDTIANAAQNYL--EKKGVACRIRFVNRLDMDTSGLLVIAKNPYTHHIMSQQMKANEITKKYVAFVKGVVVANEGEIDGAIYRSSDETIKRVVDDR--GQQSLTKFTVLERYADATMLEVSLLTGRTHQIRVHMESIGHPMLGDHLY 256
>gi|191638454|ref|YP_001987620.1| Pseudouridine synthase [Lactobacillus casei] >gi|190712756|emb|CAQ66762.1| Pseudouridine synthase [Lactobacillus casei BL23] (307 aa)
Score = 270, Expect = 5.0e-22, Identities = 80/260 (30%), Positives = 131/260 (50%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFL-RLKPIKKELKLNFLEA--KPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           M   F    E+ +I K  I+      + S++ K +++G + VN + T  NYK+   D + I +   KP         LEA  +PI L+++YED  +IVV+KP+G++  P       TL N +  +         +   + HR+DK T+GL + AK +K    L+     +   + YL L +G FK+   T+   +  +        DR+ +      +  +T ++V+E+ +    ++  L TG+ HQIRVHMA I HPV GD  Y  K
  S:     2 MTSTFTITTEQGRIDK-VITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASGDVIAISIPEAKP---------LEAIPEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPR------DRKRQAVVAAGRHAVTHFQVLERFEHYTFIKCILETGRTHQIRVHMAYIHHPVAGDPLYGPK 253
>gi|86147922|ref|ZP_01066226.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. MED222] >gi|85834247|gb|EAQ52401.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. MED222] (314 aa)
Score = 270, Expect = 5.4e-22, Identities = 81/295 (27%), Positives = 139/295 (47%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKF 300
           I ++   Q + +F+    K +  S I + ++ G+++VN K+    YKL+  D     +R+ P+  E K         LN        +IYED +++++NKP G         K       I+     + D  +LE  L HR+D+ T+G+ + AK +  L  L   +  + V KYY  L  G++K     +   +  NE   I+ ++   K ++   T+++V+E+ ++  L++   +TG+ HQIRVH    GHP+  D +Y  +                  FD       LN+L L   NIKF
  S:    13 IDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKLKAGD----LVRIPPVTIEEKTEENVPSTKLNKVSELEQCIIYEDDHMLILNKPSGTAVHGGSGLKFGA----IEALRALRPDARFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYFALVMGEWKNSCKVVNAPLLKNEVNSIVRVNPNGKASE---TRFKVLEKFQEATLIQASPITGRTHQIRVHAQYTGHPIAWDDRYGDR-----------------RFDAYTGKVGLNRLFLHAANIKF 285
>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 = 270, Expect = 5.6e-22, Identities = 85/263 (32%), Positives = 141/263 (53%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKT-TWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           M QI I  +   + +   IS  +K++S   I + IK   + +N +K    + K+ END L+    + P KK   L+       ++++YED ++ VV KP G+          +TL N +     +      +E   + HRLD+YT GL V AKN  +  +L+ ++  + V K+Y  + YG  + K  T++ FI  +   ++  E+  E K     ITKY + +  K+ +LL+I++ TG+ HQIRVHM+ IGHP++GDT Y  K ++
  S:     1 MPQIKITPDIAGERIDVLISNIYKDISREYIKRIIKENGVLINGEKVFKSSKKVFENDVLE--FEIPPPKK---LDVKAQDIHIDILYEDNDLAVVVKPSGMPSHTGPGHDENTLVNALLAKFGDLSVIGGVERPGIVHRLDRYTHGLMVIAKNDVSHQKLSLMFKNKEVDKHYKAIVYGISRFKEQTIETFIRRHPTNRLKFEVANEGKL---AITKYSLEKPLKNASLLDIKIYTGRTHQIRVHMSYIGHPIVGDTLYGYKHSY 258
>gi|91202037|emb|CAJ75097.1| similar to pseudouridine synthase C [Candidatus Kuenenia stuttgartiensis] (244 aa)
Score = 270, Expect = 5.6e-22, Identities = 70/195 (35%), Positives = 115/195 (58%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLW-NTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           L ++YED++I+V++KP GL+       K  T    +  Y+ +   K+     + HRLD+  +GL + AKN ++   L + W NTE   K YL + +G+  KK+ T+  ++  N+  Q++    + K  K   T YRV+++ K  +LLEI+LLTG+K+QIRVH+  +GHP++GD KY K+    ++   L +Y I F
  S:    16 LAILYEDEDILVIDKPAGLLTMGTDTNKTKTAYYMLNDYVRKGCVKSRKHVFIIHRLDRDASGLLLFAKNIRSKLNLQSQWQNTE---KKYLTVVHGRLAKKAGTISTYLAENK-AQVVYSTSDTKKGKLSHTVYRVLKETKYFSLLEIKLLTGRKNQIRVHLTELGHPIVGDKKYGKEKG-AYKRLALHAYSISF 206
>gi|85711025|ref|ZP_01042085.1| Pseudouridylate synthase [Idiomarina baltica OS145] >gi|85694938|gb|EAQ32876.1| Pseudouridylate synthase [Idiomarina baltica OS145] (322 aa)
Score = 270, Expect = 5.6e-22, Identities = 76/246 (30%), Positives = 129/246 (52%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKEL-KLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           L   +++ F + S S++ K I  G + V+ +        +  + L+ F  L  I  EL +    +A+PI L+++YED++I+++NKP GL+  P       TL N +   L+   D +++  A + HRLDK TTGL V A+N    T+L ++     +++ Y  +C G         +       ++  M +    K     +T YRV+E+ +   LL ++L +G+ HQIRVHMA I HP++GD  Y  +
  S:    20 LDQILAELFPDYSRSRMKKWITEGKVSVDAQVIE-----KPREKLE-FGALVAIDAELEREERYQAQPIELDIVYEDEDILIINKPAGLVVHPGAGAPDGTLLNGL---LHYDPDIDHVPRAGIIHRLDKDTTGLMVVARNIPAQTQLVDMMQKREITREYEAVCNGVMTAGGMVDEPIGRHPTKRTHMAVVSSGK---PAVTHYRVVERFRAHTLLRLRLESGRTHQIRVHMAHIRHPLVGDLTYGGR 256
>gi|116074038|ref|ZP_01471300.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9916] >gi|116069343|gb|EAU75095.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9916] (343 aa)
Score = 269, Expect = 5.9e-22, Identities = 79/256 (30%), Positives = 132/256 (51%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S ++I K I  G ++VN K       L++ D +Q+++   P  + L   +L+ +P+ L+V++ED ++IV+NKP GL   P    K  TL N +   L+   D       L   + HRLDK TTG  V AK+Q+ L +L         S+ Y+ + +G  +  S ++   I  +  + K+   +  E+   +   T + ++E+  D +LL  +L TG+ HQIRVH A + HPV+GD  Y++        P    +  +   D
  S:    52 EQSRARIQKFIDAGFVRVNGKTGKAKTPLRDGDEVQLWM---PPPEPLP--YLKPEPMDLDVLFEDDHLIVINKPAGLTVHPAPGNKDGTLVNGL---LHHCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYMAVVHGLPQGDSGSIVGAIGRHPADRKKYAVVSGES--GRYACTHWTLVERLGDYSLLRFKLDTGRTHQIRVHCAHMNHPVVGDPTYSRCRKLPIDLPGQALHAFQLGLD 304
>gi|150005860|ref|YP_001300604.1| putative RNA pseudouridylate synthase [Bacteroides vulgatus ATCC 8482] >gi|149934284|gb|ABR40982.1| putative RNA pseudouridylate synthase [Bacteroides vulgatus ATCC 8482] (308 aa)
Score = 269, Expect = 6.2e-22, Identities = 73/246 (29%), Positives = 133/246 (54%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT-WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           L DF+ +    +S SK+   + N  I V++  TT +N+ L+    +QI         ++K N     P+L ++YED  I+VV K  GL+    +++K  T  + + +Y+  K+   +    + HRLD+ T+GL + AK++KT   L + W+     + Y+ +  G  +K   T++ ++  + +  +     +N   K  +T Y+ I++    +L+E+ L TG+K+QIRVHM  +GHPV+GD +Y  +
  S:    31 LMDFLMRKMAGISRSKVKALLANRVILVDNVITTQYNFALKPGMKVQI--------SKVKNNREFKHPMLKLVYEDAYILVVEKKEGLLSVSTEHQKERTAQHILNEYV--KRSHRFNRVFVVHRLDRETSGLMMYAKDEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVESWL-TDRKLYVSSSPVDNGEGKFAVTHYKTIKRANGYSLVELDLETGRKNQIRVHMLDLGHPVVGDRRYGSE 266
>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 = 269, Expect = 6.7e-22, Identities = 72/235 (30%), Positives = 118/235 (50%)
  Q:    26 LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           LS  + +  IK G + VN ++    Y +Q  D +   L      KE  L +      L++IYED  + ++NKP+G++  P       T+ N +  ++ +    N  +   + HR+DK T+GL + AK       L      +   + YL + +G        ++  I  +E+      DR+ +      KE +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:    22 LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFEL-----PKEEVLEYQAQNIPLDIIYEDDTLAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEK------DRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR 250
>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 = 269, Expect = 6.8e-22, Identities = 83/266 (31%), Positives = 136/266 (51%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFPCLTSY 273
           KE+    +   + +   + S ++I   IK G +  N K    NYK++ ND + +       K+ ++ + L     L++ YED ++ VV KP+G++  P      +TL N +   +Y+ K+       +   + HR+D  T+GL + AKN      L      ++V + Y+ L +G       T+   I  N+ ++Q M +  + K   E +T + V+E  KD  L+E QL TG+ HQIRVHM  IG P++GD KY  K            G  GF+ P  + Y
  S:    11 KEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLNDHIVV-----TEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGL---MYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGRNKNDRQSMAVVDDGK---EAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTSEY 282
>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 = 269, Expect = 7.0e-22, Identities = 90/286 (31%), Positives = 152/286 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQ-KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF-NFDKNHFLHYLNKL 291
           + KE E   +  ++S+     S S I   I+   IKVN+K    NYKL+  D + I +    I K      +E++ I L+++YEDK++IVVNK +G++  P       TL N +  +  +    N  +   + HR+DK T+G+ V AKN ++  +L       ++++ Y  L  G+FK  S  +   +  +++ ++     E+   +  IT Y V+E+      L++ +L TG+ HQIRVHMAS+GHP++GD  Y  KK  F  +   L + K+ F +  KN ++ +   L
  S:     8 VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNNKLIKSNYKLKACDEIVITMPEAEILK------VESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNALLFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFKNDSGVIDKPLGRDKKNRLKIAITED--GRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRVHMASLGHPLVGDPLYGFKKQRFKLKGQMLHAKKLGFIHPTKNEYMEFETNL 290
>gi|171913853|ref|ZP_02929323.1| pseudouridine synthase, RluA family protein [Verrucomicrobium spinosum DSM 4136] (303 aa)
Score = 269, Expect = 7.0e-22, Identities = 86/282 (30%), Positives = 144/282 (51%)
  Q:    13 QILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN----YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMA-SIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLE 294
           Q L  ++     ++S +++   IK+G I +N K    N  L++ D + + +   P+  E+    +     LNV++ED++IIV+NKP GL+  P       TL N +   L+  K+ +     L   + HRLDK T+G  VAAK+    T L   ++   ++K YL    G     S  +++ I  +  + K++  +  E    KE +T++  +   +  AL+  +LLTG+ HQIRVHM  ++G P+LGDT Y +      + P L  +  K  F      H + KL L+
  S:    13 QRLDHYLQGELPDMSRTRLQGLIKDGHILLNGKAAKPNTPLKQGDRITMEVP-DPVPTEV----VPQDIPLNVLFEDEHIIVINKPDGLVVHPAAGNPDGTLVNAL---LFHCKNLSGIGGELRPGIVHRLDKETSGCMVAAKHDLAHTRLTEAFSQRDLTKIYLAAVNGTPSSSSGRIENRIGRHPVDRKRMALVTGEA--GKEALTEWDRVAVHQGCALIRCRLLTGRTHQIRVHMKEALGCPILGDTIYAQIQRQLIKMPRLMLHAWKLEFQ-----HPITKLGLK 286
>gi|148243331|ref|YP_001228488.1| pseudouridylate synthases, 23S RNA-specific [Synechococcus sp. RCC307] >gi|147851641|emb|CAK29135.1| Pseudouridylate synthases, 23S RNA-specific [Synechococcus sp. RCC307] (316 aa)
Score = 269, Expect = 7.4e-22, Identities = 79/256 (30%), Positives = 132/256 (51%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S ++I K I+ G ++VN         L+  D +++++   P  + L   +L+ +P+ L+V++ED+++IV+NKP GL   P    K  TL N +   L+   D       L   + HRLDK TTG  V AK+Q+ L +L         S+ YL + +G    +S T+   I  +  + K+   +  +N   +   T + + E+  D +LL  +L TG+ HQIRVH A   HPV+GD  Y++      + P    + ++   D
  S:    34 EQSRARIQKFIEAGYVRVNGTTGRAKTPLRHGDEIKLWM---PPPEPLP--YLQPEPMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGL---LHHCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQQALVKLQVQIQKRVASREYLAVVHGVPAGESGTIVGAIGRHPVDRKKYAVVSSDN--GRYACTHWSLQERLGDYSLLRFKLDTGRTHQIRVHCAHRNHPVVGDPTYSRCRKLPIELPGQALHAVQLGLD 286
>gi|116492157|ref|YP_803892.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus ATCC 25745] >gi|116102307|gb|ABJ67450.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus ATCC 25745] (296 aa)
Score = 268, Expect = 7.5e-22, Identities = 63/193 (32%), Positives = 117/193 (60%)
  Q:    85 VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI-FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLT-SYKIKF 277
           ++YE+ +++VVNKP G+    ++  ++ ++ N ++ Y  + ++    EA   HRLD++T+G  + AKN   +  LN   +T+ +++ YLC+  G  ++   T+   I F  ++K+  +I+  N  +   IT Y+V+ Q ++ +L+++ L TG+ HQIRVH++ +GHP++GD  YN       Q P L  S+KI+F
  S:    87 ILYENSDLMVVNKPTGVKTHANQPHELGSMMNFLQAYFKDTEN----EAYNVHRLDQFTSGALLVAKNPVVVPILNRQISTKVINRTYLCVVSGHLEQSKGTINVPIGFDPDDKRKRQINGLNPLSA--ITHYQVLAQYENSSLIQVDLETGRTHQIRVHLSYLGHPIIGDPLYNLDNT---QQPMLLHSWKIRF 272
>gi|160872397|ref|ZP_02062529.1| ribosomal large subunit pseudouridine synthase C [Rickettsiella grylli] >gi|159121196|gb|EDP46534.1| ribosomal large subunit pseudouridine synthase C [Rickettsiella grylli] (315 aa)
Score = 268, Expect = 7.6e-22, Identities = 75/255 (29%), Positives = 134/255 (52%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI---FLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I K+   Q L +F+    K L  S++ + I+ G++++  K+   +Y+LQE D +++    L   P KK++ LN  +AK +   +I+EDK+++V+NKP G+         +      I+ +   +    +LE  L HRLD+ T+G  + AK +  L EL+ L     + K Y+ L  G +     ++ + ++ N+ +    + R     K  +TK+ + +   D  L+    +TG+ HQIRVH   + HP++GD KY  K
  S:     9 ITKDYSGQRLDNFLISRLKGLPKSRLYRIIRKGELRIYKKRVKPDYRLQEGDIIRVPPLSLSGLPTKKKV-LNEKQAKFLEKTIIFEDKHLLVLNKPSGMAVHGGSGITLGV----IEAFRLIRPQLKFLE--LVHRLDRETSGCLLMAKKRSILKELHELLRLNGIKKTYIALVSGHWPPSLLSVAEPLYKNQRQSGERMVRVQPEGKRSLTKFSIQQYYSDSTLVTATPITGRTHQIRVHAQCVNHPIIGDEKYGNK 260
>gi|56419100|ref|YP_146418.1| ribosomal large subunit pseudouridine synthase [Geobacillus kaustophilus HTA426] >gi|56378942|dbj|BAD74850.1| ribosomal large subunit pseudouridine synthase [Geobacillus kaustophilus HTA426] (299 aa)
Score = 268, Expect = 7.7e-22, Identities = 73/251 (29%), Positives = 126/251 (50%)
  Q:    13 QILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           Q+LKD  + S K     ++   +K     +N +   W   L E D LQ++   +P    +   + E    L++++ED +++V+NK  G+   P +  +  TL N +  YL  +      +    HRLD+ T+G  + AK+      L+ +    A+ + Y+ L +G+   KS T+  F  +  ++      R +K   + +T YRVI+     +L+E+ L TG+ HQIRVH+A +GHP++GD  Y  K  F
  S:    24 QLLKDVWAASKKLAHRWRMEHGVK-----LNGQAVPWKTVLNERDRLQLY-AYEPEPSFIVPEYRE----LSILWEDDHLLVLNKEAGIDIHPSEPGQTGTLANAVAFYL--QSQAILTKVRHIHRLDRDTSGAILFAKHPLAGATLDRMLAHRAIKRTYVALVHGRLSPKSGTI--FAPIGRDRHHPTRRRVSKTGAKAVTHYRVIKTFPSTSLVELSLETGRTHQIRVHLAHLGHPLVGDVLYGGKPVF 260
>gi|90579091|ref|ZP_01234901.1| putative 23S rRNA ribosomal pseudouridinesynthase [Vibrio angustum S14] >gi|90439924|gb|EAS65105.1| putative 23S rRNA ribosomal pseudouridinesynthase [Vibrio angustum S14] (314 aa)
Score = 268, Expect = 8.0e-22, Identities = 84/297 (28%), Positives = 143/297 (48%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKE-----LKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKF 300
           I I  +   Q + +F+    K +  S I + ++ G+++VN K+    YKLQ+ D +++     P K+E      KLN + A+    +IYED +++++NKP G         K       I+     + D  +LE  L HR+D+ T+G+ + AK +  L +L   +  + V KYY  L  G++K     +   +  NE   I+ ++ + K +    T+++V+E+     L++   +TG+ HQIRVH    GHP+  D +Y          P   +Y  K           L +L L   NIKF
  S:    11 IEISDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLVRVPPVFVPEKEEQAPVSTKLNKV-AELEHCIIYEDDHMLILNKPSGTAVHGGSGLKFGA----IEALRALRPDARFLE--LVHRIDRDTSGILLVAKKRSALRQLQEQFRNKTVQKYYFALVMGEWKANCRKVTAPLLKNEVNSIVRVNPQGKASD---TRFKVLERFPQATLVQASPVTGRTHQIRVHCQYEGHPIAWDDRYGD--------PRFDAYTKKTG---------LGRLFLHAANIKF 285
>gi|115525546|ref|YP_782457.1| RluA family pseudouridine synthase [Rhodopseudomonas palustris BisA53] >gi|115519493|gb|ABJ07477.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas palustris BisA53] (458 aa)
Score = 268, Expect = 8.2e-22, Identities = 77/256 (30%), Positives = 130/256 (50%)
  Q:     2 IQIFIKKEEENQILKD-FISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILN----VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE--EKQIMEIDRE-NKFNKEIITKYRVIE-QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +Q  +   +EN +  D F+   F  LS S I + ++ G+++VN K+     +L+E  S++I  L+L   K    L+  E K +      ++YED +++V+NKP GL  Q             +   L   +D    +  L HRLDK T G  + AK +   T L   + + +  K Y  L  G  K K   +  ++  +E  +  IM +    ++     +T Y V+E   + +A + ++ +TG+ HQ+R HMA IGH ++GD KY
  S:   132 VQTVVVTADENAMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEGQSVRIPPLQLDAPKGGGNLSEAEQKTLAALKAMILYEDADVMVLNKPAGLAVQGGSGT-----TRHVDLMLEVMRDSKGQKPRLVHRLDKETAGCLLVAKTRFAATALTGSFRSRSARKVYWALVAGVPKPKQGRISTYLAKDESEDDSIMRVAAHGDEGASHAVTYYAVVETSAQKLAWVSLKPVTGRTHQLRAHMAHIGHAIIGDPKY 392
>gi|90407030|ref|ZP_01215220.1| Predicted pseudouridylate synthase, Rlu family protein [Psychromonas sp. CNPT3] >gi|90311901|gb|EAS39996.1| Predicted pseudouridylate synthase, Rlu family protein [Psychromonas sp. CNPT3] (303 aa)
Score = 268, Expect = 8.6e-22, Identities = 73/252 (28%), Positives = 132/252 (52%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKEL-------KLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I +E   Q + +F+    K +  S I + I+ G+++VN K+   +YKLQ  D     +R+ P+K          KLN + A+    ++YED  ++++NKP G+                I+     + D  +LE  L HRLDK T+G  + AK +  L  L+     + ++K YL L  G + KK  ++K+ +  + +  ++++   +   K+  T+++++++     L+E   +TG+ HQIRVH A  GH + GD +Y
  S:     4 ISQENAKQRIDNFLRLHLKGVPKSLIYRIIRKGEVRVNKKRIKPDYKLQPGD----IVRIPPVKVSAENPLPSPKLNAI-AQLESRIVYEDDALLILNKPSGIAVHGGSGLSFGA----IEGLRALRPDARFLE--LVHRLDKATSGCLLIAKKRSMLRALHEQLRNKTMNKQYLALVKGSWDKKDRSVKEPLLKDSQNSVVKV---SALGKQAETRFKIMQRYHGATLVEASPVTGRTHQIRVHCACKGHNIAGDDRY 248
>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 = 268, Expect = 8.7e-22, Identities = 85/272 (31%), Positives = 135/272 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           I KE + + +++F+ +    LS   I  +  +  IKV+      NY ++  + ++I L     KKE + N    K  + ++YED +I+V+NK   ++  P ++    TL N I  Y  E      +   L  RLD  T+GL +  KNQ     L+N   T+   K YL + +G  ++K  T+   I+   E  I  +  E    +E IT Y+VIE  K   L+E  L TG+ HQIRVH++S+GHP+ GD+ Y  +         L +Y + F
  S:     8 ITKEYDKRKIREFLKEELG-LSSRLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELS----KKESQ-NIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVR--LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVVDER--GQESITHYKVIESYKGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISRQALHAYGLDF 269
>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 = 268, Expect = 8.7e-22, Identities = 72/235 (30%), Positives = 118/235 (50%)
  Q:    26 LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           LS  + +  IK G + VN ++    Y +Q  D +   L      KE  L +      L++IYED  + ++NKP+G++  P       T+ N +  ++ +    N  +   + HR+DK T+GL + AK       L      +   + YL + +G        ++  I  +E+      DR+ +      KE +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:    22 LSRGQANDQIKQGLVLVNDQQKKAKYTVQAGDVICFEL-----PKEEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEK------DRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR 250
>gi|71907635|ref|YP_285222.1| ribosomal large subunit pseudouridine synthase C [Dechloromonas aromatica RCB] >gi|71847256|gb|AAZ46752.1| ribosomal large subunit pseudouridine synthase C [Dechloromonas aromatica RCB] (334 aa)
Score = 268, Expect = 8.9e-22, Identities = 76/260 (29%), Positives = 142/260 (54%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIK-KELKLNFLEA----KPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAV--SKYYLCLCYGKFKKKSDTLK----DFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           + +EE  Q L +F+ +  K +  S I + +++G+++VN K+    Y+L   D++    R+ PI+  E   N ++     +  L +IYED+ +++++KP G+                I+    ++    +LE  L HRLD+ T+G+ +  K +  LT L++++        K YL L  G++   +  +K     ++    E+++  +D + K +    T +R++ +  + +LLE QL TG+ HQIRVH+A +G P+LGD KY   G+F  
  S:    14 VGEEELGQRLDNFLIRRCKGVPKSHIYRILRSGEVRVNSKRVDATYRLCVGDNI----RIPPIRIAERPQNEVDEAAKERVDLPIIYEDEAMLIIDKPEGIAVHGGSGVSFGV----IEALRRQRPQAKFLE--LAHRLDRETSGVLLVGKKRLALTALHDMFREHGAGADKRYLVLVKGRWMNNTQHVKLPLHKYLTEGGERRV-SVDAQGKASH---TVFRLLARWPEASLLEAQLKTGRTHQIRVHLAHLGFPILGDEKY---GDFAL 267
>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 = 268, Expect = 8.9e-22, Identities = 72/235 (30%), Positives = 118/235 (50%)
  Q:    26 LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           LS  + +  IK G + VN ++    Y +Q  D +   L      KE  L +      L++IYED  + ++NKP+G++  P       T+ N +  ++ +    N  +   + HR+DK T+GL + AK       L      +   + YL + +G        ++  I  +E+      DR+ +      KE +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:    22 LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFEL-----PKEEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEK------DRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR 250
>gi|159906031|ref|YP_001549693.1| RluA family pseudouridine synthase [Methanococcus maripaludis C6] >gi|159887524|gb|ABX02461.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C6] (297 aa)
Score = 268, Expect = 9.0e-22, Identities = 85/245 (34%), Positives = 136/245 (55%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           L D +  +F ELS   I K  K   I VN K  +   KL+EN+++ + +       +  +N ++ + + LNVIYED ++++V+KP+ ++  P KN    TL N I  +  +K +    +     RLD  TTGL + AKN  +   L    +   + K Y+ +  G+   K   ++D I LN++    E+    K +K   TKY+VIE+ K+ ++LEI LLTG+ HQIRVH++S+G+ +LGD  Y K
  S:    21 LIDVLKDNF-ELSNKMIKKFDKEKKIFVNSKIISLKSKLKENETVSVEI-------DCGINNIDPEELPLNVIYEDDDLLIVDKPKNMVVHPTKNVLSKTLANAISNH--QKINNQNYKIRFVSRLDMDTTGLLIIAKNSYSHQHLAKQMDEGILEKIYVAVVNGRLDLKEGIIEDSIDLNDDGIKRELSNSGKISK---TKYKVIEELKNASVLEINLLTGRTHQIRVHLSSLGNYILGDILYGK 253
>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 = 268, Expect = 9.2e-22, Identities = 89/263 (33%), Positives = 136/263 (51%)
  Q:     6 IKKEEENQILK-DFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY--NK-----KGNF------GFQFP 268
           IK  EEN+ L+ D    +  E S S +++ IKN  + VN++     YK++  D +Q       I +   L+ +     L +IYED ++ VVNKP+G++  P       TL N I  ++ +    N  +   + HR+DK T+GL + AKN K    L      +   + YL + +G+      T++  I  N +      DR+ +      K  +T + V+E      L+ ++L TG+ HQIRVHM  IGHPV GD  Y  NK     KG F      GF+ P
  S:     4 IKITEENKDLRLDKALANQTEYSRSLLTELIKNDKVFVNNEAKKAKYKVKTGDRIQF-----EIPQAEVLDVVAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGELANDKGTIEAPIGRNLK------DRKKQAVVSGGKPAVTHFEVLEGFVGYTLIALRLETGRTHQIRVHMHYIGHPVAGDPLYGPNKTLTPNKGQFLHAETLGFEHP 274
>gi|170289613|ref|YP_001739851.1| RluA family pseudouridine synthase [Thermotoga sp. RQ2] >gi|170177116|gb|ACB10168.1| pseudouridine synthase, RluA family [Thermotoga sp. RQ2] (304 aa)
Score = 268, Expect = 9.6e-22, Identities = 88/298 (29%), Positives = 156/298 (52%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKT-TWNYKLQENDSLQI-FLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIK 299
           ++I + +E   + L  F+  + K+  LS I K I+ G + VN K+     + L+E D+++I ++ L+ + K      L   P+ L++I+E+ N +V+NKP G+   P K   + TL   I+  LY  +++ + E  L HRLDK T+GL + AKN++    L  ++    + K Y+ L  G      + LK  I L+ ++ + EI                ++  K+++LL +++ TG+KHQIR H++ IG PV+GD  Y   G+  F       Y +K +F  ++ + + +    E K+ K
  S:     1 MRIDVTRENFYRRLDKFLRNTLKDFPLSTIYKLIRKGKVYVNGKRVRDPGFDLEEGDTVEIKYVNLENLPKRSDKKDLTPVPMKLDIIHENDNYLVLNKPAGIAIHPGKGVHVATL---IEGLLYYGQEQGF-EPFLVHRLDKDTSGLLIVAKNREAARVLTEMFRGRNMEKEYIALVKGV---PENNLKITIPLDGQEAVSEIVS--------------VKPLKNVSLLRVKIHTGRKHQIRRHLSQIGFPVVGDDTY---GDRQFNREFRRKYALKRHFLHSYRMRFFDPWAEEEKDFK 277
>gi|33864373|ref|NP_895933.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9313] >gi|33641153|emb|CAE22283.1| putative pseudouridylate synthase specific to ribosomal large subunit [Prochlorococcus marinus str. MIT 9313] (324 aa)
Score = 267, Expect = 1.0e-21, Identities = 78/256 (30%), Positives = 127/256 (49%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S S I K I+ G ++VN         L++ D +++++   P  + L     E  P L+V++ED+++IV+NKP GL   P    +  TL N +   L+   D       L   + HRLDK TTG  V AK+Q+ L +L         S+ YL + +G       T+   I  +  + K+   +  +    +   T + ++E+  D +LL  +L TG+ HQIRVH A IGHP++GD  Y++        P    + ++   D
  S:    40 EQSRSHIQKFIEAGLVRVNGITGRAKTPLRQGDEVELWM---PPPEPLPYLQPEEMP-LDVLFEDRHLIVINKPAGLTVHPAPGNRNGTLVNGL---LHHCSDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQEQIQKRIASRNYLAVVHGAPSGDQGTIVAAIGRHPVDRKKYAVVTEDG--GRHACTHWTLVERLADYSLLRFKLDTGRTHQIRVHCAHIGHPIVGDPIYSRCRKLPMDLPGQILHAVQLGLD 292
>gi|150402179|ref|YP_001329473.1| RluA family pseudouridine synthase [Methanococcus maripaludis C7] >gi|150033209|gb|ABR65322.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C7] (298 aa)
Score = 267, Expect = 1.0e-21, Identities = 81/245 (33%), Positives = 137/245 (55%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           L D +  +F ELS   I K  K   I VN K  +   KL+EN+++ + +       +  +N ++ + + LN+IYED ++++V+KP+ ++  P KN    TL N +  +  +K +    +    +RLD  TTGL + AK+  +   L    +   + K Y+ +  G    K   ++D I LN++    E+    K +K   TKY+VIE+ K+ ++LEI LLTG+ HQIRVH+++IG+P++GD  Y +
  S:    21 LIDVLRNNF-ELSNKMIKKFDKEKKIFVNSKNISLKSKLKENETVSVEI-------DCGINTIDPENLALNIIYEDDDLLIVDKPKNMVVHPTKNVLSKTLANAVSNH--QKINNQNYKIRFVNRLDMDTTGLLIIAKDPYSHQHLAKQMDEGILEKIYIAVVNGHLDLKEGIIEDSIDLNDDGIKRELSNVGKISK---TKYKVIEELKNASILEINLLTGRTHQIRVHLSNIGNPIIGDVLYGE 253
>gi|154491501|ref|ZP_02031127.1| hypothetical protein PARMER_01111 [Parabacteroides merdae ATCC 43184] >gi|154088302|gb|EDN87347.1| hypothetical protein PARMER_01111 [Parabacteroides merdae ATCC 43184] (303 aa)
Score = 267, Expect = 1.0e-21, Identities = 77/249 (30%), Positives = 131/249 (52%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT-WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +EEN +L  F+     E S S +   + +G I VN   T+ +N  L   + + I       + +++ N     P+L +++ED ++IVVNK  GL+       K  T  + + +Y+ +   +N +   + HRLD+ T+GL + AKN +    L + WN+   ++ Y+ +  G+ +K SD +   +  N + Q+      +   KE IT+YR++      +LLE+ L TG+K+QIR  M SIGH + GD KY
  S:    24 KEENTLLP-FLFGLLNEQSKSSVKALLAHGQISVNGTVTSQFNTPLTPGNEVLISYE----RGKVEFN----NPLLTIVWEDDDLIVVNKKEGLLSVSSTRVKERTALHLLSEYVKKTDPRNKI--FVLHRLDRDTSGLMMFAKNLQVQKALQSNWNSAITARTYVAVVEGRPEKDSDLIVSNLTENAKMQVYVTAEGD--GKEAITRYRLLHSNGAYSLLELDLETGRKNQIRAQMQSIGHSIAGDYKY 260
>gi|150009274|ref|YP_001304017.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides distasonis ATCC 8503] >gi|149937698|gb|ABR44395.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides distasonis ATCC 8503] (359 aa)
Score = 267, Expect = 1.0e-21, Identities = 76/229 (33%), Positives = 126/229 (55%)
  Q:    29 SKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEAN-----LCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++I  + + G I VN K    NY+++  D + I +  +P ++EL++   E  P LN++YED +++VVNKP GL+  P       TL N +  YL   KD  Y + +     L HR+DK T+GL V AK  +  + L+  +  +   + Y  L +G  ++    ++  I  +  ++  M +  E    K  +T Y V+E+   ++L+E +L TG+ HQIRVHM  IGH +  D +Y
  S:    60 NRIQLAAEAGCILVNDKPVKSNYRVKPLDVVSIVMD-RP-RRELEI-IPEDIP-LNIVYEDDDLLVVNKPAGLVVHPGHGNYTGTLVNALAYYL---KDDPYYDPSDPRLGLVHRIDKDTSGLLVVAKRPEAKSNLSLQFFNKTTKRKYRALVWGIVQEDEGRIEGNIGRDPRDRMQMTVFPEGDQGKTAVTHYTVLERLGYVSLVECRLETGRTHQIRVHMKYIGHTLFNDERY 287
>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 = 267, Expect = 1.0e-21, Identities = 83/266 (31%), Positives = 135/266 (50%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFPCLTSY 273
           KE+    +   + +   + S ++I   IK G +  N K    NYK++ ND + +       K+ ++ + L     L++ YED ++ VV KP+G++  P      +TL N +   +Y+ K+       +   + HR+D  T+GL + AKN      L      ++V + Y+ L +G       T+   I  N+ ++Q M +  + K   E +T + V+E  KD  L+E QL TG+ HQIRVHM  IG P++GD KY  K            G  GF+ P    Y
  S:    11 KEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLNDHIVV-----TEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGL---MYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGRNKNDRQSMAVVDDGK---EAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTGEY 282
>gi|153853839|ref|ZP_01995195.1| hypothetical protein DORLON_01186 [Dorea longicatena DSM 13814] >gi|149753589|gb|EDM63520.1| hypothetical protein DORLON_01186 [Dorea longicatena DSM 13814] (296 aa)
Score = 267, Expect = 1.1e-21, Identities = 61/176 (34%), Positives = 105/176 (59%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN 258
           L++IYED++IIV+NKP G+   P  N   ++L N +  Y Y+K+DK ++    C+RLD+ T+GL V +K+  + + L+ +     V + YL +  G+    S T+   +   +E  I+E   + +  +E IT Y++I +    +L+ ++L TG+ HQIR+HM  +G P++GD  YN
  S:    81 LDIIYEDEDIIVINKPAGMPIHPSMNNYYNSLANALAWY-YQKQDKPFI-FRCCNRLDRDTSGLTVVSKHLVSGSILSTMTKNREVHREYLAVVKGRVTPSSGTICAPL-ARKEGTIIERMVDFEHGEEAITHYKLIREANGHSLVSLKLETGRTHQIRIHMKYLGFPLIGDYLYN 253
>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 = 267, Expect = 1.1e-21, Identities = 72/235 (30%), Positives = 118/235 (50%)
  Q:    26 LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           LS  + +  IK G + VN ++    Y +Q  D +   L      KE  L +      L++IYED  + ++NKP+G++  P       T+ N +  ++ +    N  +   + HR+DK T+GL + AK       L      +   + YL + +G        ++  I  +E+      DR+ +      KE +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGHPV GD  Y  +
  S:    22 LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFEL-----PKEEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQVLTEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEK------DRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR 250
>gi|66043991|ref|YP_233832.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae B728a] >gi|63254698|gb|AAY35794.1| Pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae B728a] (320 aa)
Score = 267, Expect = 1.2e-21, Identities = 81/263 (30%), Positives = 131/263 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPI-KKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           +  E   Q L    ++ F E S S++S  IK+G + V+         L+  D +     L+ I ++E +  ++     L++IYED  I+V+NKP GL+  P       TL N +   L+   D  N   A + HRLDK TTGL V AK  +  T+L     + +VS+ Y C+  G                +++Q M +    +  K+ ++ YRV+E+ +    + ++L TG+ HQIRVHMA I +P++GD  Y  +    F+ P
  S:    11 VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVD------GGALRPRDIVHGGAVLELIAEQEAQGEWVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNAL---LHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQRQRMAV---MEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLVGDPAYGGR----FRIP 259
>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 = 267, Expect = 1.3e-21, Identities = 78/254 (30%), Positives = 129/254 (50%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD------KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIM-EIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           +  F+++  +  + +K+ ++I+   + VN K    NYK+  ND + +     P         LE + I L++++ED+ ++V+NKP G++  P       TL   +   LY  ++      K  L   + HRLDK T+GL V AK+  T   L   +      K Y  L +G  K  S T++  I+ ++ +++IM     E++  K  IT Y V E     +LL++QL TG+ HQIR H+  +GH +  D  Y  K      FP
  S:    37 IDKFLTRQVENATRNKVQEAIEESRVLVNGKPIKSNYKVCPNDEIFVIFTHPPAPD------LEPENIPLDIVFEDEFLLVINKPAGMVVHPAYANWTGTLAGAV---LYHTQNRLSETGKEALRPGIVHRLDKDTSGLIVVAKDDATHYALAKQFAERTTEKIYTALVWGCPKPPSGTIQTNIWRSKRDRKIMANYPFESETGKPAITDYEVKEDFHWFSLLDLQLHTGRTHQIRAHLQHLGHAIFSDEVYGGKSVRKLGFP 290
>gi|149190361|ref|ZP_01868634.1| 23S rRNA pseudouridine synthase D [Vibrio shilonii AK1] >gi|148835850|gb|EDL52814.1| 23S rRNA pseudouridine synthase D [Vibrio shilonii AK1] (324 aa)
Score = 266, Expect = 1.3e-21, Identities = 74/256 (28%), Positives = 126/256 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           +K  +  Q L   +++ F + S S++ + + +G I VN +  T    K+   + + +   L+  ++       EA+ I LN++YED +IIV+NKPR  +  P       T+ N +  +     +     A + HRLDK TTGL V AK     T L        +++ Y  +  GK        K     + ++ +M +   N+  K  +T YRV E  ++   + ++L TG+ HQIRVHM+ + HP+LGD+ Y  + 
  S:    11 VKDSQLGQRLDQAVAELFADFSRSRLKEWLLDGKIAVNGEVITKPRTKVMGGELITVQAELEDEER------FEAQDIPLNIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHFPAIAE--VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGKMTAGGMVDKAIGRHSTKRTLMAV---NELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDSAYGGRA 257
>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 = 266, Expect = 1.3e-21, Identities = 77/258 (29%), Positives = 132/258 (51%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++  K+++E   L  ++S+  ++LS SK    I N  + VN      +Y +   D +++  +L  I+ E+ L  +     L+++YED+ ++VVNKPR ++  P      DT+ N +  +     D  +Y    + HRLDK T+GL V AK  +T   L+       V++ YL L  G F KK  T+   I  +   ++ M +    K     +   R  +  + ++ L+  L TG+ HQIRVH++ +G+P+LGD  Y  K
  S:    15 ELIPKEKDEGLRLDLYLSEQIEDLSRSKAKMLINNNSVMVNDNWVKASYSITSGDVVKVDTQL--IQSEITL--IPQSIPLDIVYEDEYLLVVNKPRNMVVHPGAGNYRDTMVNALLYHCQNLSDGTSYERPGIVHRLDKDTSGLLVVAKQNETHDILSEEIKNRRVARTYLALVIGDFSKKKATIDLPIGRDPRNRKKMAVVHGGKRAITKVEMLRSFQNPEKISYLKCSLETGRTHQIRVHLSHLGYPLLGDPVYRGK 270
>gi|15643702|ref|NP_228748.1| ribosomal large subunit pseudouridine synthase C [Thermotoga maritima MSB8] >gi|4981478|gb|AAD36021.1|AE001757_14 ribosomal large subunit pseudouridine synthase C [Thermotoga maritima MSB8] (304 aa)
Score = 266, Expect = 1.3e-21, Identities = 85/276 (30%), Positives = 149/276 (53%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT-WNYKLQENDSLQI-FLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKF 277
           +++ + +E   + L  F+    K++ LS I K I+ G + VN K+    ++ L+E D +++ ++ L+ + K  +   L   P+ L+V+YED + +V+NKP  +   P K   + TL   I+  LY  ++K +    L HRLDK T+GL V AKN++    L  L+    + K Y+ L  G            +  N  K  + +D      +E +++   ++  KD++LL +++ TG+KHQIR H++ IG PV+GD  Y         +  +G +   L SY++KF
  S:     1 MRMEVTRENFYRRLDKFLRNQLKDVPLSVIYKLIRKGKVYVNRKRVKDPSFDLEEGDVVELRYVNLENLPKRSEKKDLTPVPMKLDVLYEDDHYLVLNKPPNIAIHPGKGVHVATL---IEGLLYYGQEKGF-SPFLVHRLDKETSGLLVVAKNREAARILTELFKGRNIEKEYVTLVRG------------VPENNMKITIPLD-----GQEAVSEIVSVKPLKDVSLLRVKIHTGRKHQIRRHLSQIGFPVVGDDTYGDRHFNREFRKRYGLKRQFLHSYRMKF 265
>gi|120553810|ref|YP_958161.1| RluA family pseudouridine synthase [Marinobacter aquaeolei VT8] >gi|120323659|gb|ABM17974.1| ribosomal large subunit pseudouridine synthase D [Marinobacter aquaeolei VT8] (325 aa)
Score = 266, Expect = 1.3e-21, Identities = 77/258 (29%), Positives = 131/258 (50%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           Q  +  E  ++ L    ++   E S S++   IK+G + VN K      K+   DSL   L  +P   E+++ + EA+PI L+++YED++++V+NKP GL+  P       TL N +  Y  E +  N   A + HRLDK T+G+ V A++    T L +   T  + + Y  +  G     +          ++++ M +    K     +T YR++E+     L+  +L +G+ HQIRVHMA + HP++GD  Y  +
  S:    10 QFTVPPELSDKRLDQAAAELMPEHSRSRLQSWIKSGALTVNGKSRKPRDKVMMGDSLA--LDAEP---EVQVTW-EAEPISLDIVYEDEHLLVINKPAGLVVHPAAGHTDGTLVNALLNYAPEVE--NLPRAGIVHRLDKDTSGIMVVARSLIAHTSLVDQLQTRTMGREYEAVVVGALTGGATVDAPIGRHPQDRKRMAVVSSGK---PAVTHYRLLERFAAHTLVRCKLESGRTHQIRVHMAHVRHPLVGDPAYGGR 257
>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 = 266, Expect = 1.5e-21, Identities = 78/263 (29%), Positives = 130/263 (49%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
           ++ + I      Q +   +++     S  KI+  IK+GD  ++HK      K+   + + +      IK E    +L    +++V+YED+ II+VNKP  L+  P  +    TL N +  Y  +    N   A + HRLDK T+GL V A+++     L     T ++S+ Y  + YG       T+   I  + + +I +   E+   K+ +T YRVIE+      +++ L TG+ HQIRVH++ IGHP++ D  Y  K  F
  S:     3 LLSVIIPNRFIGQRIDAAMAQMLPNYSRVKITYWIKSGDALIHHKTFKPKEKVLGGEVITL-----SIKIEKTNAWLAQDIVIDVVYEDEAIIIVNKPVNLVTHPGVSNWTGTLANALLHY--DSSLANLDRAGIVHRLDKNTSGLMVVARSEYAQKYLTRQLQTHSISREYSAIVYGHMIS-GGTVDKPIGRDPKDRIRQTVTES--GKDALTHYRVIERFAHHTHVKVMLETGRTHQIRVHLSFIGHPLIADPMYGGKIRF 255
>gi|16331032|ref|NP_441760.1| hypothetical protein slr1629 [Synechocystis sp. PCC 6803] >gi|3915482|sp|P74346|Y1629_SYNY3 Uncharacterized RNA pseudouridine synthase slr1629 (RNA-uridine isomerase) (RNA pseudouridylate synthase) >gi|1653527|dbj|BAA18440.1| slr1629 [Synechocystis sp. PCC 6803] (327 aa)
Score = 266, Expect = 1.5e-21, Identities = 74/254 (29%), Positives = 127/254 (50%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT-WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           L  ++++   ELS S+  K I++G ++ N       N  L+  D L +      I + + L+ +     L+++YED+ +I++NKP GL+  P       T+ N +  +  +      ++   + HRLDK TTG  V AK +  L  L      +   + Y  + YG  K+   T+   +  +  ++Q M I    K  +E +T +R++E+  + + LE QL TG+ HQIRVH   +GHP++GD  Y   G+     P
  S:    34 LDKWLAEQLPELSRSRCQKLIESGQVQRNGLVCQDKNLILKTGDRLVV-----NIPELIPLDVVAQNIPLDILYEDEQLIIINKPAGLVVHPGPGHPDGTVVNALLAHCPDLAGIGGVQRPGIVHRLDKDTTGAMVVAKTELALHNLQVQLKEKTARRLYWGIVYGSPKEIQGTVNLPVGRHPGDRQKMGIVPVEKGGREAVTHWRLLERIGNHSWLEFQLETGRTHQIRVHSKQMGHPLVGDNLYTSPGSVNVNLP 285
>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 = 266, Expect = 1.5e-21, Identities = 84/272 (30%), Positives = 135/272 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           I KE + + +++F+ +    LS   I  +  +  IKV+      NY ++  + ++I L     KKE + N    K  + ++YED +I+V+NK   ++  P ++    TL N I  Y  E      +   L  RLD  T+GL +  KNQ     L+N   T+   K YL + +G  ++K  T+   I+   E  I  +  E    +E IT Y+VIE  +   L+E  L TG+ HQIRVH++S+GHP+ GD+ Y  +         L +Y + F
  S:     8 ITKEYDKRKIREFLKEELG-LSSRLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELS----KKESQ-NIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVR--LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVVDER--GQESITHYKVIESYEGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEDFISRQALHAYGLDF 269
>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 = 266, Expect = 1.5e-21, Identities = 73/266 (27%), Positives = 134/266 (50%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI--------LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           + +++ EE++  +  ++++   +LS S+I + I+ G ++VN K  T         S +I L+   +   + L   EA+P+        L+++YED  ++++NKP GL+  P       TL N +  +  +      ++   + HRLDK TTG    AK       +      +   + YL + YG  K  S  +   I  + ++++ M +    +  +  IT +++ E+  +  L+  QL TG+ HQIRVH A +GHP++GD  Y    + G   P
  S:     4 EFYLEVEEDSARIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCT---------SKKINLK---VGDRITLEVPEAQPLEIQAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHSHGTLVNALLAHCPDLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQAKTARREYLGVVYGAPKTASGKVDLPIGRHPQDRKKMAVVPIEEGGRSAITHWQIQERLGNFTLIHFQLETGRTHQIRVHSAKMGHPIVGDPVYGSGRSVGVNLP 267
>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 = 266, Expect = 1.5e-21, Identities = 82/252 (32%), Positives = 133/252 (52%)
  Q:    26 LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF 277
           LS S+I   I  G + +N         +   D   I +R+ P  + ++L   E  P L+++YED++I+VVNK RGL+  P       TL +     L +K D        L   + HRLDK TTGL V AK+++ +  L        V + Y  L +G     +  ++  I  +  +++ M ++   K  ++ +T +RV+E+ +  ALLE +L TG+ HQIRVH++ IGHPV+GD  Y  +K + G     L + ++ F
  S:    27 LSRSRIQALIDEGQVTLNGAMPKARQAVNPGDV--IVVRV-PDPEPMEL-VPEDIP-LDIVYEDEDILVVNKQRGLVVHPAAGHWTGTLVHA----LLDKVDDLEGIGGELRPGIVHRLDKDTTGLLVVAKSERAMASLQEQIRDHMVQRVYWALVHGNSMPDTGRIEAPIGRHPRDRKRMAVN--PKTGRDAVTYFRVLERYRGYALLECRLETGRTHQIRVHLSFIGHPVVGDPLYGPRKPHLGMPPQALHARQLSF 274
>gi|94970372|ref|YP_592420.1| ribosomal large subunit pseudouridine synthase D [Acidobacteria bacterium Ellin345] >gi|94552422|gb|ABF42346.1| ribosomal large subunit pseudouridine synthase D [Acidobacteria bacterium Ellin345] (333 aa)
Score = 266, Expect = 1.5e-21, Identities = 73/261 (27%), Positives = 136/261 (52%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQ------PDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKD----MALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNF 263
            I +  ++ N  L  ++     ++S +++   I +  I V+ K +  +YKL+ ++ + +    +P      L  +     L+V+YED ++ V+NKP G++         ++  +   +N  + ++    +    +   + HRLDK T+GL V AKN     +L   +++  V K Y+ L +G  KK   T+   I  +  ++     R +   ++ ++ Y V E+ +      AL+E+++ TG+ HQIRVHMAS+GHPV+GDT Y   G  
  S:     6 HIQVSADDANIRLDQYLVSHLPDVSRARVQALIDDEKILVDGKSSKPSYKLRGSEVIDVVGEYQPPP----LRAIPEDIPLDVVYEDDDLAVINKPAGMMVHVGAGATEEERNRGTLVNALLYRFRALSEVGGDMRPGIVHRLDKETSGLIVVAKNDVAHRKLAEQFSSRRVHKKYVALVHGWPKKLKGTINLPIARDMSRRTRMTTRGSG-GRDALSHYEVKEKIESPYGKFALVEVKIETGRTHQIRVHMASLGHPVVGDTLYGAPGEL 271
>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 = 266, Expect = 1.6e-21, Identities = 84/249 (33%), Positives = 129/249 (51%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFPCLTSY 273
           E S S+I   IK   + VN K    NYK++ ND L I    + ++ +++   L     L++ YED+++ +V KP+G++  P       TL N +   +Y+ KD       +   + HR+DK T+GL + AKN      L      ++V + Y  L +G       T+   I  NE ++Q M++    K   E +T + V+E   D  L+E QL TG+ HQIRVHM  IG P++GD KY  +            G  GF+ P    Y
  S:    28 EWSRSQIQDLIKEDLVTVNEKVIKSNYKVKLND-LIIVTEKEVVEADIQPENLN----LDIYYEDEDVAIVYKPKGMVVHPSPGHYSGTLVNGL---MYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYTALVHGNIPHDYGTIDAPIGRNEKDRQSMDVVDNGK---EAVTHFNVLEHFNDYTLIECQLETGRTHQIRVHMKYIGFPLVGDPKYGPRKTLDIGGQALHAGVIGFEHPVTHEY 282
>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 = 266, Expect = 1.6e-21, Identities = 88/259 (33%), Positives = 147/259 (56%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I + ++KE +N  L  ++SK F++ S S +   I  G + VN+KK   NYKL+  D++++ +       E KL  +E + I L++IYEDK++IVVNKP+ ++  P       TL N +  +  +    N +    + HR+DK T+G+ V AKN  +   L   +   ++S+ Y+ L  G  K +  T++  I  +   +I M + ++ +     +T Y+VIE+ K+  L+E +L TG+ HQIRVHM+ I HP++GD  Y  K
  S:     4 ISLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDQGSVLVNNKKKKRNYKLKVGDNIEVNI------PEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQGTIEAPIGRHPVDRIKMAVVKDGR---HAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYK 256
>gi|42629156|ref|ZP_00154705.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Haemophilus influenzae R2846] (324 aa)
Score = 266, Expect = 1.6e-21, Identities = 76/255 (29%), Positives = 129/255 (50%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++ E+  Q L   +++ F E S S++   I+   +K+N + T     K+   + ++I + ++   +       EA+ I LN++YED +IIV+NKP+ L+  P       T+ N +   LY     + +  A + HRLDK TTGL V AK     T+L        +++ Y  +  G   K     +       ++ +M +   +   K  +T YR++E  ++   L ++L TG+ HQIRVHMA I HP+LGD  Y  +
  S:    10 VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVEVEDETR------FEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNAL---LYHYPPISEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLMAV---HPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGR 255
>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 = 266, Expect = 1.6e-21, Identities = 76/238 (31%), Positives = 125/238 (52%)
  Q:    23 FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKT-LTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
             ELS S  ++ IK+G + VN +     Y +QE D +   +    +     L ++     L ++Y+D+++ VVNKP+G++  P       TL N +   +Y  KD       L   + HR+DK T+GL + AKN    L     L + +++ KY+  + +G        ++  I  +E+      DR+ +      K  +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGH V GD  Y  +
  S:    19 LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVTYHVPEPEV-----LEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL---MYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYW-AIVHGNLPNDRGVIEAPIGRSEK------DRKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSVAGDEVYGPR 250
>gi|91216414|ref|ZP_01253381.1| ribosomal large subunit pseudouridine synthase [Psychroflexus torquis ATCC 700755] >gi|91185552|gb|EAS71928.1| ribosomal large subunit pseudouridine synthase [Psychroflexus torquis ATCC 700755] (345 aa)
Score = 266, Expect = 1.6e-21, Identities = 71/250 (28%), Positives = 128/250 (51%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI---DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           K +E   +  F+    +  + +K+ ++ K+G+I VN      NYK++  D +++ L   P +     N L  + I L+++YED  ++VVNK  G++  P       TL N +  +     + +     L HR+DK T+GL V AK +  +  L+  +  +   + Y+ + +G   ++  T++  I  N + ++  I     +    K  +T Y+VIE+   + L+  QL TG+ HQIRVH+  IGH +  D +Y
  S:    23 KGQEPLRVDKFLMNFIENATRNKVQQAAKDGNIYVNGIPVKQNYKVKAGDEVKVLLAYPPYE-----NLLTPEDIPLDIVYEDDALLVVNKAAGMVVHPGHGNYSGTLINALVYHFENLPNNSSDRPGLVHRIDKDTSGLLVVAKTEAAMAYLSRQFFHKTSKREYVAIAWGNLNEEEGTIEGNIGRNPKNRLQNIVYLGDDADQGKPAVTHYKVIERLGYVTLISCQLETGRTHQIRVHLKHIGHTLFNDERY 271
>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 = 266, Expect = 1.7e-21, Identities = 81/257 (31%), Positives = 129/257 (50%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDK 281
           +LS S+ S+ IK G + VN K     Y ++E D   I    +P  +E  L+ +     L ++YED+++ V+NKP+G++  P       TL N +   L+  KD       +   + HR+DK T+GL + AKN +    L      +   + Y+ L +G        ++  I  +E+      DR+ +      K  +T ++V+E+    +L+E+ L TG+ HQIRVHMA IGHPV GD  Y  K     Q   L +  + F   K
  S:    21 DLSRSQASEQIKAGLVLVNGKTQKAKYAVKEGD---IIHYERP--QEEVLDCVAQNIPLEIVYEDEDVAVINKPQGMVVHPSVGHPSGTLVNAL---LFHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDQAHQALAKELKEKKSLRQYIALVHGNLPNDRGVIEAPIGRSEK------DRKKQTVTAKGKPAVTHFKVLERFGQYSLVELTLETGRTHQIRVHMAYIGHPVAGDPLYAPKKTLKGQGQFLHAKTLGFTHPK 271
>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 = 265, Expect = 1.7e-21, Identities = 75/235 (31%), Positives = 126/235 (53%)
  Q:    23 FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           F + S S+I   IK G + V+ KK+    K +E   +   + L+ + +++  +  E  P L+++YED++I+VVNKP GL+  P    +  TL N I   L+   +  ++  A + HRLDK TTGL V AK     TEL +     ++ + Y  +  G         +      + +Q M ++  N   K+ +T YR++++ K+   + ++L TG+ HQIRVHM+ I  P+LGD +Y
  S:    28 FSDYSRSRIQAWIKEGVLLVDGKKS----KAKEKLFVGEVISLETLVEDIDDHQPEDIP-LDIVYEDEDILVVNKPSGLVVHPAVGHRSGTLMNAI---LFHCPESAHVPRAGIVHRLDKETTGLMVVAKTLAAQTELVSQLQDRSMGREYEAVAIGIMTGGGTVNEPIGRHPQNRQKMAVEPLN--GKDAVTHYRLLQRFKNHTHIRLKLETGRTHQIRVHMSHIQFPLLGDPQY 253
>gi|183219523|ref|YP_001837519.1| pseudouridine synthase (Uracil hydrolyase) [Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'] >gi|189909665|ref|YP_001961220.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)'] >gi|167774341|gb|ABZ92642.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)'] >gi|167777945|gb|ABZ96243.1| Pseudouridine synthase (Uracil hydrolyase) [Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'] (237 aa)
Score = 265, Expect = 1.7e-21, Identities = 61/178 (34%), Positives = 113/178 (63%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEID--RENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           L++IYED++++VV+KP GL+    ++EK  T    +  Y+ +  +++     + HRLD+ T+G+ V AK +     L + W  +   K Y+ + +G++K+K  T+K ++  ++  ++  +D  +E K+++   TKY+V+++    +LLEI L+TG+K+QIRVH A   HP++GDTKY  +
  S:    14 LSIIYEDRDLLVVDKPAGLLTIATESEKSKTAYASLMDYVKKGSERSKNRIFIVHRLDRDTSGILVFAKTEIAKQTLQDNW--DQTKKNYIAVTHGQWKEKQGTIKSYLTESKAHRVYSVDDPKEGKYSE---TKYKVLKESNLYSLLEIDLITGRKNQIRVHFAENKHPIVGDTKYGSE 188
>gi|150003134|ref|YP_001297878.1| ribosomal large subunit pseudouridine synthase D [Bacteroides vulgatus ATCC 8482] >gi|149931558|gb|ABR38256.1| ribosomal large subunit pseudouridine synthase D [Bacteroides vulgatus ATCC 8482] (358 aa)
Score = 265, Expect = 1.8e-21, Identities = 75/255 (29%), Positives = 126/255 (49%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE--KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++ + K +    +  ++ +     S ++I K+   G I  N K    +YK++  D L + +     +     + +     L+++YED +++VVNKP GL+  P       TL N I  +L +  K D N  +  L HR+DK T+GL V AK     T L   +  +   + Y  L +G  +    T++  I  N +++  M +  +    K  +T YRV+E+   + L+E  L TG+ HQIRVHM  IGH +  D +Y
  S:    32 RVVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMMD----RPRYDNDIIPEDIPLDIVYEDNDLMVVNKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPKYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGVVENNEGTIEGNIGRNPKDRMQMAVLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMKHIGHTLFNDERY 285
>gi|53711780|ref|YP_097772.1| ribosomal large subunit pseudouridine synthase D [Bacteroides fragilis YCH46] >gi|60680012|ref|YP_210156.1| ribosomal large subunit pseudouridine synthase [Bacteroides fragilis NCTC 9343] >gi|52214645|dbj|BAD47238.1| ribosomal large subunit pseudouridine synthase D [Bacteroides fragilis YCH46] >gi|60491446|emb|CAH06196.1| ribosomal large subunit pseudouridine synthase [Bacteroides fragilis NCTC 9343] (357 aa)
Score = 265, Expect = 1.8e-21, Identities = 75/231 (32%), Positives = 117/231 (50%)
  Q:    27 SLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           S ++I K+ ++G +  N K    +YK++  D + + +       E+     E  P L+++YEDK ++VVNKP GL+  P       TL N I  +L +  D   N     L HR+DK T+GL V AK     T L   +  +   + Y  L +G   +   T+   I  N +++  M +  +    K  +T YRV+E+   + L+E  L TG+ HQIRVHM  IGH +  D +Y
  S:    55 SRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVMMDRPRYDNEI---IPEDIP-LHIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHLKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGVQFFNKTTKRRYRALVWGIVDQDEGTIVGSIARNPKDRMQMAVMADPTQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGHVLFNDERY 284
>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 = 265, Expect = 1.8e-21, Identities = 88/259 (33%), Positives = 148/259 (57%)
  Q:     2 IQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I + ++KE +N  L  ++SK F++ S S +   I  G++ VN+KK   NYKL+  D++++ +       E KL  +E + I L++IYEDK++IVVNKP+ ++  P       TL N +  +  +    N +    + HR+DK T+G+ V AKN  +   L   +   ++S+ Y+ L  G  K +  T++  I  +   +I M + ++ +     +T Y+VIE+ K+  L+E +L TG+ HQIRVHM+ I HP++GD  Y  K
  S:     4 ISLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKKKKRNYKLKVGDNIEVNI------PEPKLLEIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLNHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQGTIEAPIGRHPVDRIKMAVVKDGR---HAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYK 256
>gi|71735208|ref|YP_273032.1| ribosomal large subunit pseudouridine synthase D(pseudouridine synthase) (Uracil hydrolyase) [Pseudomonas syringae pv. phaseolicola 1448A] >gi|71555761|gb|AAZ34972.1| Ribosomal large subunit pseudouridine synthase D(Pseudouridine synthase) (Uracil hydrolyase) [Pseudomonas syringae pv. phaseolicola 1448A] (320 aa)
Score = 265, Expect = 1.8e-21, Identities = 81/263 (30%), Positives = 131/263 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPI-KKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           +  E   Q L    ++ F E S S++S  IK+G + V+         L+  D +     L+ I ++E +  ++     L++IYED  I+V+NKP GL+  P       TL N +   L+   D  N   A + HRLDK TTGL V AK  +  T+L     + +VS+ Y C+  G                +++Q M +    +  K+ ++ YRV+E+ +    + ++L TG+ HQIRVHMA I +P++GD  Y  +    F+ P
  S:    11 VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVD------GGVLRPRDIVHGGAVLELIAEQEAQGEWVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNAL---LHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQRQRMAV---MEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLVGDPAYGGR----FRIP 259
>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 = 265, Expect = 1.9e-21, Identities = 81/277 (29%), Positives = 133/277 (48%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK---KGNFGFQFPCLTSYKIKF 277
           +  I + + E  Q L   +S +  +LS + + + I +  I+VN +    +  +Q  D ++IFL   P+ K   +   E  P L+VIYED ++++VNK  G++  P       TL N +            L   + HRLDK T+GL V AK+ +    L        + K YL L  G +++ + T+   I  N   ++ M +  E ++    +T Y+V+E     +L+   L TG+ HQIRVH +    P+L D  Y     K  FG +   L +Y + F
  S:     7 LTTIQVGEAEAGQRLDRLVSANMPDLSRTYVQQLITDLHIRVNGRGAKASLPVQIGDQIEIFL---PLAKPTDI-VAEDLP-LDVIYEDADVLLVNKAAGMVVHPAPGHTTGTLVNALLYRYPHLTTSGDLRPGIVHRLDKETSGLLVIAKHDQARMMLTEQQMARRMHKKYLALVEGHWREPTGTIDAPIGRNPNNRLRMMVMPEGRY---AVTHYQVLEVLGPYSLVRATLETGRTHQIRVHFSYRNRPILNDALYGHRKPKETFGIERHFLHAYHLGF 279
>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 = 265, Expect = 1.9e-21, Identities = 91/286 (31%), Positives = 153/286 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQ-KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-KKGNFGFQFPCLTSYKIKF-NFDKNHFLHYLNKL 291
           + KE E   +  ++S+     S S I   I+   IKVN K    NYKL+  D + I +   P  + LK+   E++ I L+++YEDK++IVVNK +G++  P       TL N +  +  +    N  +   + HR+DK T+G+ V AKN ++  +L       ++++ Y  L  G+FK  S  +   +  +++ ++     E+   +  IT Y V+E+      L++ +L TG+ HQIRVHMAS+GHP++GD  Y  KK  F  +   L + K+ F +  KN ++ +   L
  S:     8 VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNDKLIKNNYKLKACDEIVITM---PEAETLKV---ESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNALLFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFKNDSGIIDKPLGRDKKNRLKIAITED--GRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRVHMASLGHPLVGDPLYGFKKQKFKLKGQMLHAKKLGFIHPTKNEYMEFETNL 290
>gi|89073417|ref|ZP_01159941.1| putative 23S rRNA ribosomal pseudouridine synthase [Photobacterium sp. SKA34] >gi|89050904|gb|EAR56378.1| putative 23S rRNA ribosomal pseudouridine synthase [Photobacterium sp. SKA34] (314 aa)
Score = 265, Expect = 1.9e-21, Identities = 84/297 (28%), Positives = 143/297 (48%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKE-----LKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKF 300
           I I  +   Q + +F+    K +  S I + ++ G+++VN K+    YKLQ+ D +++     P K+E      KLN + A+    +IYED +++++NKP G         K       I+     + D  +LE  L HR+D+ T+G+ + AK +  L +L   +  + V KYY  L  G++K     +   +  NE   I+ ++ + K +    T+++V+E+     L++   +TG+ HQIRVH    GHP+  D +Y          P   +Y  K           L +L L   NIKF
  S:    11 IDISDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLVRVPPVFVPEKEEQAPVSTKLNKV-AELEHCIIYEDDHLLILNKPSGTAVHGGSGLKFGA----IEALRALRPDARFLE--LVHRIDRDTSGILLVAKKRSALRQLQEQFRNKTVQKYYFALVMGEWKANCRKVTAPLLKNEVNSIVRVNPQGKASD---TRFKVLERFPLATLVQASPVTGRTHQIRVHCQYEGHPIAWDDRYGD--------PRFDAYTKKTG---------LGRLFLHAANIKF 285
>gi|116493188|ref|YP_804923.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus ATCC 25745] >gi|116103338|gb|ABJ68481.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus ATCC 25745] (294 aa)
Score = 265, Expect = 1.9e-21, Identities = 64/198 (32%), Positives = 114/198 (57%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           L++I+EDKN ++VNKP GL   P  +++ DTL NRIK +    + KN +  +L  RLD++T+G+ + A++Q + + L+       + K YL +  G  + +  T    + L  +    E+  + +   +  T ++V+++ ++  L++I L TG+ HQIRVH A+ GHP++GD  Y+   + G +   L +  I+F FD
  S:    78 LDIIFEDKNWLLVNKPAGLTAVPGPSDREDTLVNRIKGHWQAIESKNMM-PHLVTRLDRFTSGITLVARHQVSNSLLSEQVAHHKIKKIYLAMVDGVVQAEKGTFNQSLGLAADGIHREVRDDGQ---QATTSFKVLKRFENQTLVQIHLKTGRTHQIRVHFANAGHPLVGDQLYDGPMDRGIKRQALHASSIRF-FD 270
>gi|145641509|ref|ZP_01797087.1| SfhB [Haemophilus influenzae R3021] >gi|145273800|gb|EDK13668.1| SfhB [Haemophilus influenzae 22.4-21] (324 aa)
Score = 265, Expect = 2.0e-21, Identities = 76/255 (29%), Positives = 129/255 (50%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++ E+  Q L   +++ F E S S++   I+   +K+N + T     K+   + ++I + ++   +       EA+ I LN++YED +IIV+NKP+ L+  P       T+ N +   LY     + +  A + HRLDK TTGL V AK     T+L        +++ Y  +  G   K     +       ++ +M +   +   K  +T YR++E  ++   L ++L TG+ HQIRVHMA I HP+LGD  Y  +
  S:    10 VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVEVEDETR------FEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNAL---LYHYPPISEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLMAV---HPIGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGR 255
>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 = 265, Expect = 2.0e-21, Identities = 69/229 (30%), Positives = 123/229 (53%)
  Q:    29 SKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-----MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           SKI K+ K G+I VN+     NYK++ ND + +     P +  L    ++    ++++YED +++VVNK  G++  P       TL N +  ++    + +     L HR+DK T+GL V AK ++ +T L   +  +   + Y+ L +G  +    T++  I  + + ++     ++ D E K  K  +T ++V+E+   + L+  +L TG+ HQIRVHM  IGH +  D +Y
  S:    48 SKIQKAAKEGNIFVNNVIVKSNYKVKANDVVTVLFAHPPYELLLTPEDID----IDIVYEDDDLLVVNKQPGMVVHPGHGNYSGTLINALIHHIDNLPNNSSNRPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTTEREYVALVWGNIEDDEGTIEGHIGRHPKNRLQNTVFLDEDAEEK-GKAAVTHFKVLERFGYVTLVSCKLETGRTHQIRVHMKFIGHTLFNDERY 276
>gi|145637336|ref|ZP_01792996.1| SfhB [Haemophilus influenzae PittHH] >gi|145269428|gb|EDK09371.1| SfhB [Haemophilus influenzae PittHH] (324 aa)
Score = 265, Expect = 2.0e-21, Identities = 76/255 (29%), Positives = 129/255 (50%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++ E+  Q L   +++ F E S S++   I+   +K+N + T     K+   + ++I + ++   +       EA+ I LN++YED +IIV+NKP+ L+  P       T+ N +   LY     + +  A + HRLDK TTGL V AK     T+L        +++ Y  +  G   K     +       ++ +M +   +   K  +T YR++E  ++   L ++L TG+ HQIRVHMA I HP+LGD  Y  +
  S:    10 VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVEVEDETR------FEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNAL---LYHYPPISEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLMAV---HPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGR 255
>gi|85058561|ref|YP_454263.1| 23S rRNA pseudouridine synthase D [Sodalis glossinidius str. 'morsitans'] >gi|84779081|dbj|BAE73858.1| ribosomal large subunit pseudouridine synthase D [Sodalis glossinidius str. 'morsitans'] (326 aa)
Score = 265, Expect = 2.0e-21, Identities = 80/255 (31%), Positives = 125/255 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQ---ENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           + + +  Q L   +++ F + S S+I   I +G ++VN + T    +     E+  +Q F+   P          EA+ I LN++YED +I+V+NKPR L+  P       T+ N +  Y     D     A + HRLDK TTGL V AK     T L        +++ Y  +  G       TL+  I  +  K+  M +   +   K  +T YR++E  +    L ++L TG+ HQIRVHMA I HP++GD  Y  +
  S:    11 VSESQLGQRLDQALAELFPDYSRSRIKAWILDGLVRVNRRVTAVPKEKMLGGESVEIQAFIEEAP--------RWEAQAIPLNIVYEDDDILVINKPRDLVVHPGAGNADGTVLNALLHYFPPIVD--VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTA-GGTLEQPIARHATKRTHMAV---HPMGKPAVTNYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLVGDPLYGGR 256
>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 = 265, Expect = 2.1e-21, Identities = 76/238 (31%), Positives = 125/238 (52%)
  Q:    23 FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKT-LTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
             ELS S  ++ IK+G + VN +     Y +QE D +   +    +     L ++     L ++Y+D+++ VVNKP+G++  P       TL N +   +Y  KD       L   + HR+DK T+GL + AKN    L     L + +++ KY+  + +G        ++  I  +E+      DR+ +      K  +T++ V+E+  D +L+E+QL TG+ HQIRVHMA IGH V GD  Y  +
  S:    19 LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVTYHVPEPEV-----LEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNAL---MYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYW-AIVHGNLPNDRGVIEAPIGRSEK------DRKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSVAGDEVYGPR 250
>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 = 265, Expect = 2.1e-21, Identities = 88/263 (33%), Positives = 136/263 (51%)
  Q:     6 IKKEEENQILK-DFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY--NK-----KGNF------GFQFP 268
           IK  EEN+ L+ D    +  E S S +++ IKN  + VN++     YK++  D ++       I +   L+       L +IYED ++ VVNKP+G++  P       TL N I  ++ +    N  +   + HR+DK T+GL + AKN K    L      +   + YL + +G+      T++  I  N +      DR+ +      K  +T + V+E+     L+ ++L TG+ HQIRVHM  IGHPV GD  Y  NK     KG F      GF+ P
  S:     4 IKITEENKDLRLDKALANQTEYSRSLLTELIKNDKVFVNNEAKKAKYKVKTGDRIEF-----EIPQAEVLDVAAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGELANDKGTIEAPIGRNLK------DRKKQAVVSGGKPAVTHFEVLERFVGYTLIALRLETGRTHQIRVHMHYIGHPVAGDPLYGPNKTLTPNKGQFLHAETLGFEHP 274
>gi|163751081|ref|ZP_02158312.1| RluC [Shewanella benthica KT99] >gi|161329242|gb|EDQ00241.1| RluC [Shewanella benthica KT99] (319 aa)
Score = 265, Expect = 2.1e-21, Identities = 81/297 (27%), Positives = 146/297 (49%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI--------FLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKNIKF 300
           + I ++   Q + +++    K +  S+I + ++ G+++VN K+    YKLQ+ D ++I          R  P  K  K++ LE +    +++EDK IIV+NKP G+                I+     +  + +LE  L HRLDK T+G+ + AK +  L  L++    + + K Y  L  G ++ +   +K  +     K    I R N+  KE  T+++++++ +   L++   +TG+ HQIRVH    GHP+  D KY+++                  FD    +H LN+L L    ++F
  S:    13 VTIDEDHLGQRIDNYLMTKLKGVPKSRIYRIVRKGEVRVNKKRIKPEYKLQDGDIVRIPPVRVSDKSDRPGPSAKLTKVSQLEDR----IVFEDKFIIVLNKPSGIAVHGGSGVDFGV----IEAMRALRPTQKFLE--LVHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQKDYQALVKGTWQARDKVIKAPLLKLTLKSGERIVRVNQEGKECETRFKILQRYQGATLVQASPVTGRTHQIRVHCQYAGHPIACDDKYSEQ-----------------RFDDTMRVHGLNRLFLHAAQLRF 290
>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 = 265, Expect = 2.1e-21, Identities = 74/277 (26%), Positives = 146/277 (52%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKK-TTWNYKLQENDSLQIFL-RLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLE-ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQF--PCLTSYKIKF 277
           M    ++ EE  + L  ++S++   LS S+I + I+ G++ +N +  TT    ++  D + + +  ++P++       ++A+ I L+++YED +++++NKP GL+  P       TL N +  +         ++   + HRLDK TTG    AK       L      +   + YL + YG  K ++  + + I  + ++++ M +    K  +  +T ++++E+  +  L+  QL TG+ HQIRVH A IGHP++GD  Y+   + G +     L ++++K 
  S:     1 MTAFNLQVEETGERLDRYLSENLPNLSRSRIQQLIEQGNVHLNEQICTTKKITVKAGDRITLEIPEVQPLQ-------VQAQDIPLDILYEDDHLLILNKPAGLVVHPAPGHPDGTLVNALLAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYHSLQAQLQAKTARREYLGVVYGAPKTENGKIDEPIGRHPQDRKKMAVVPIEKGGRNAVTHWQILERLGNQTLVLFQLETGRTHQIRVHSAKIGHPIVGDPIYSSAHSVGVKLNGQALHAWRLKL 277
>gi|114331690|ref|YP_747912.1| pseudouridine synthase, RluA family protein [Nitrosomonas eutropha C91] >gi|114308704|gb|ABI59947.1| ribosomal large subunit pseudouridine synthase C [Nitrosomonas eutropha C91] (354 aa)
Score = 265, Expect = 2.2e-21, Identities = 76/260 (29%), Positives = 140/260 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI--FLRL-KPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLK----DFIFLNEEKQIMEIDRENKFNK--EIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           + +  E Q + +F+ K+ K++    I + +++G ++VN K+    Y+L  ND ++I   L+L KPI ++      +     + +Y+D  ++V+NKP G                 I++   ++ D  +LE  L HRLD+ T+G+ + A+ ++TL EL+       V K+YL L  GK+K     ++     ++    E+++      N  +K  +  T + + +  +  +LL+ +L TG+ HQIRVH+A +G P+ GD KY   G+FG 
  S:    40 VDETAEGQRIDNFLIKALKDIPRRHIYQLLRSGQVRVNSKRIDAGYRLLLNDKVRIPPVLKLAKPISRQAPYRAEQ----FDTLYQDDYLLVINKPAGTAVHGGSGISYGV----IEQLRKQRPDWKFLE--LVHRLDRETSGVLLLARKRQTLLELHKQIREGTVRKHYLTLVRGKWKNSLQNVRLPLYKYLTAEGERRVAIATGRNDHDKVQQAYTLFALQKNWEAFSLLDAELKTGRTHQIRVHLAHLGFPIAGDDKY---GDFGL 295
>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 = 264, Expect = 2.2e-21, Identities = 84/272 (30%), Positives = 134/272 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           I KE + + +++F+ +    LS   I  +  +  IKV+      NY ++  + ++I L     KKE + N    K  + ++YED +I+V+NK   ++  P ++    TL N I  Y  E      +   L  RLD  T+GL +  KNQ     L+N   T+   K YL + +G  ++K  T+   I+   E  I  +  E    +E IT Y+VIE      L+E  L TG+ HQIRVH++S+GHP+ GD+ Y  +         L +Y + F
  S:     8 ITKEYDKRKIREFLKEELG-LSSRLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELS----KKESQ-NIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVR--LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVVDER--GQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISRQALHAYGLDF 269
>gi|28898835|ref|NP_798440.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio parahaemolyticus RIMD 2210633] >gi|153839692|ref|ZP_01992359.1| ribosomal large subunit pseudouridine synthase C [Vibrio parahaemolyticus AQ3810] >gi|34395766|sp|Q87N15|RLUC_VIBPA Ribosomal large subunit pseudouridine synthase C (rRNA-uridine isomerase C) (rRNA pseudouridylate synthase C) >gi|28807054|dbj|BAC60324.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio parahaemolyticus RIMD 2210633] >gi|149746785|gb|EDM57773.1| ribosomal large subunit pseudouridine synthase C [Vibrio parahaemolyticus AQ3810] (315 aa)
Score = 264, Expect = 2.2e-21, Identities = 75/277 (27%), Positives = 136/277 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------GNFGFQFPCLTSYKIKFNFDKN 282
           I ++   Q + +F+    K++  S I + ++ G+++VN K+    YKL+  D     +R+ P+  E K   +     LN        +IYED +++++NKP G         K       I+     +    +LE  L HR+D+ T+G+ + AK +  L  L   +  + V K+Y  L  G++K     +   +  NE   I+ ++   K ++   T+++++E+ +   L++   +TG+ HQIRVH    GHP+  D +Y  +      G  G     L +  IKF    N
  S:    13 IDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKAGD----LVRIPPVTVEKKEEDVAPSTKLNKVAELEHMIIYEDDHMLILNKPSGTAVHGGSGLKFGA----IEALRALRPQARFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKKFYFALVMGQWKSSCKVVNAPLLKNEVNSIVRVNPNGKPSE---TRFKILEKFEQATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQLGLDRLFLHAANIKFQHPSN 290
>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 = 264, Expect = 2.3e-21, Identities = 92/292 (31%), Positives = 156/292 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGD-------TKYNKKGN------FGFQFPCLTSYKIKFNFDKNHFLHYLNKLNLEVKN 297
           + +E+ +  L  +IS+ ++ELS S I K IK+  IKVN K     Y ++  D ++I L   P  +E+ +   E  P L ++YED+++IVV+KP+G++  P       TL N +   L+  K++       +   + HR+DK T+GL V AKN      L   +     ++ Y  +  G  ++K   +   I  +   ++      +   K  +T ++V+E  +D   +E +L TG+ HQIRVH++ IG+P++GD       +K+N KG       FGF  P    Y ++F  D      Y NK+   ++N
  S:     8 VLEEDVDNRLDLYISEQYEELSRSYIQKLIKDHHIKVNGKIEKAKYMIKLGDEIEINL---PQVEEVTIE-PENIP-LTIVYEDEDVIVVDKPQGMVVHPAPGNYSGTLVNAL---LFHCKNQLSDVNGPMRPGIVHRIDKDTSGLLVVAKNNAAHEILAEQFRAHTNTRKYHAIVVGNIREKEAAVDAPIGRHPVDRLKRAVMND--GKHAVTHFKVLEVFRDFTYIEAKLETGRTHQIRVHLSYIGNPLVGDPLYGAKSSKFNLKGQILHAKVFGFIHPKTKEY-MEFTSD---LPEYFNKVLRVLRN 303
>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 = 264, Expect = 2.3e-21, Identities = 84/272 (30%), Positives = 134/272 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           I KE + + +++F+ +    LS   I  +  +  IKV+      NY ++  + ++I L     KKE + N    K  + ++YED +I+V+NK   ++  P ++    TL N I  Y  E      +   L  RLD  T+GL +  KNQ     L+N   T+   K YL + +G  ++K  T+   I+   E  I  +  E    +E IT Y+VIE      L+E  L TG+ HQIRVH++S+GHP+ GD+ Y  +         L +Y + F
  S:     8 ITKEYDKRKIREFLKEELG-LSSRLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELS----KKESQ-NIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVR--LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVVDER--GQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEDFISRQALHAYGLDF 269
>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 = 264, Expect = 2.3e-21, Identities = 72/235 (30%), Positives = 118/235 (50%)
  Q:    26 LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN------KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           LS S+ +  IK   + VN       Y +Q  D +        I +E  L++      L+++Y+D  ++++NKP+G++  P       TL N +   LY  KD       +   + HR+DK T+GL + AK  K    L +    +   + Y+ + +G   K    +        E  I   D++ K        KE +T+++V+E+    +L+E+QL TG+ HQIRVHMA IGHP+ GD  Y  +
  S:    22 LSRSQANDQIKQKRVLVNGSPKKAKYIVQVGDCISYH-----IPEESSLDYQAQDIPLDIVYQDDVLVIINKPQGMVVHPSAGHSTGTLVNAL---LYHVKDLSSINGVIRPGIVHRIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRGVI--------EAPIGRSDKDRKKQTVTAKGKEALTRFKVLERFGRYSLVELQLETGRTHQIRVHMAYIGHPLAGDPLYGPR 250
>gi|86135602|ref|ZP_01054183.1| ribosomal large subunit pseudouridine synthase D [Tenacibaculum sp. MED152] >gi|85819775|gb|EAQ40932.1| ribosomal large subunit pseudouridine synthase D [Polaribacter dokdonensis MED152] (345 aa)
Score = 264, Expect = 2.3e-21, Identities = 69/246 (28%), Positives = 127/246 (51%)
  Q:    12 NQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++ L +FI  + +    +K+ ++ K G++ VN      N+K++  D +++ L   P +     N L A+ I L++IYED  +IVVNKP G++  P       TL N +  ++      +     L HR+DK T+GL V AK +  +  L+  +      + Y  L +G  ++    ++  I  + + ++ M +  +  F K  +T ++V+E+   + L++ +L TG+ HQIR H   IGH +  D +Y
  S:    32 DKFLMNFIENATR----NKVQQAAKAGNVLVNDIAVKSNHKVKPKDVVRVVLAYPPAE-----NLLVAEDIPLDIIYEDDAVIVVNKPAGMVVHPGHGNYSGTLVNGLIHHIENLPTNSNERPGLVHRIDKDTSGLLVVAKTEFAMAHLSKQFFDRTTERLYYALVWGNIEEDEGRIEGNIGRSLKNRLQMAVFPDGDFGKHAVTHFKVLERLTYVTLVQCKLETGRTHQIRAHFKHIGHTLFNDERY 270
>gi|153810858|ref|ZP_01963526.1| hypothetical protein RUMOBE_01242 [Ruminococcus obeum ATCC 29174] >gi|149833254|gb|EDM88336.1| hypothetical protein RUMOBE_01242 [Ruminococcus obeum ATCC 29174] (288 aa)
Score = 264, Expect = 2.4e-21, Identities = 73/202 (36%), Positives = 121/202 (59%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL--YEKKDKNYLEANL-------CHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEID-RENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK-------KGNFGFQFPCLTSYKIKF--------NFDKNHF 284
           L++IYED +I+++NKP G++ QPD     DT    + +YL  Y  ++ +  E NL       C+RLDK T+G+  A K+   L EL+ L++   V K YLC+  GK  + S  ++ ++  +     + +   + K  + I T+Y  I   +   LL+++L+TG+ HQIR H+AS GHP+ GD KY         + ++G +   L +Y++ F        N  + HF
  S:    42 LDIIYEDTDILLINKPAGMLSQPD-----DTKEPSMVEYLIGYLLQNGSLTEENLRTFHPSVCNRLDKNTSGVIAAGKSLAGLQELSTLFHDRTVHKDYLCIVKGKLTR-SRHIRGYLHKDANLNKVSVSPTKEKDAQPIETQYTPICNNEHATLLKVRLITGRTHQIRAHLASEGHPLAGDAKYGSQEFNRYFRDHYGLKHQLLHAYRLTFPELEGKLHNLSEKHF 262
>gi|162533081|ref|YP_001621404.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas syringae pv. tomato str. DC3000] >gi|118201618|gb|ABK79681.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas syringae pv. tomato str. DC3000] (320 aa)
Score = 264, Expect = 2.5e-21, Identities = 80/263 (30%), Positives = 131/263 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPI-KKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           +  E   Q L    ++ F E S S++S  IK+G + V+         L+  D +     L+ I ++E +  ++     L++IYED  I+V+NKP GL+  P       TL N +   L+   D  N   A + HRLDK TTGL V AK  +  T+L     + +VS+ Y C+  G                +++Q M +    +  K+ ++ YRV+E+ +    + ++L TG+ HQIRVHMA + +P++GD  Y  +    F+ P
  S:    11 VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVD------GGVLRPRDIVHGGAVLELIAEQEAQGEWVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNAL---LHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQRQRMAV---MEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHVNYPLVGDPAYGGR----FRIP 259
>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 = 264, Expect = 2.5e-21, Identities = 76/253 (30%), Positives = 132/253 (52%)
  Q:    25 ELSLSKISKSIKNGDIKVNH-KKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFK-KKSDTLKDFIFLNEEKQIME--IDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           E S S + + I++G + V   K    + K++  D L I LR  P  +  K      +  L+++YED+++IVVNKP GL+  P       TL N +   L      +++  A + HRLDK T+GL V A+ ++T+ +L ++     VS+ Y+ L +G ++  K+  ++  I  +   ++    +D E    K   T   +++  +   L++ +L TG+ HQIRVHMA +GHP++ D  Y        Q   L + ++ F
  S:    60 EFSRSYLQQLIEDGGVLVKGLKAIKTSAKVKAGDELTIELRPTPQSQAFK----PEEMALDIVYEDRHLIVVNKPAGLVVHPAPGNWSGTLLNGL---LAHDPQASFMPRAGIVHRLDKDTSGLMVVARQRQTMDQLVSMIAARTVSREYIALAHGTWEGAKTRQVEAPIGRDPRNRLRMAVVDLEKNSGKAASTVISLLDNAEKHCLVKCKLHTGRTHQIRVHMAFLGHPLVSDEVYGGAVAGSLQRQALHACRLAF 310
>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 = 264, Expect = 2.5e-21, Identities = 84/272 (30%), Positives = 133/272 (48%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           I KE + + +++F+ +    LS   I  +  +  IKV+      NY ++  + ++I L     KKE + N    K  + ++YED +I+V+NK   ++  P ++    TL N I  Y  E      +   L  RLD  T+GL +  KNQ     L+N   T+   K YL + +G   +K  T+   I+   E  I  +  E    +E IT Y+VIE      L+E  L TG+ HQIRVH++S+GHP+ GD+ Y  +         L +Y + F
  S:     8 ITKEYDKRKIREFLKEELG-LSSRLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELS----KKESQ-NIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVR--LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLAEKEGTINRPIYRPAEDTIKRVVDER--GQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISRQALHAYGLDF 269
>gi|68248781|ref|YP_247893.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 86-028NP] >gi|145635280|ref|ZP_01790983.1| ribosomal large subunit pseudouridine synthase D [Haemophilus influenzae PittAA] >gi|68056980|gb|AAX87233.1| ribosomal large subunit pseudouridine synthase D [Haemophilus influenzae 86-028NP] >gi|145267424|gb|EDK07425.1| ribosomal large subunit pseudouridine synthase D [Haemophilus influenzae PittAA] (324 aa)
Score = 264, Expect = 2.5e-21, Identities = 76/255 (29%), Positives = 129/255 (50%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++ E+  Q L   +++ F E S S++   I+   +K+N + T     K+   + ++I + ++   +       EA+ I LN++YED +IIV+NKP+ L+  P       T+ N +   LY     + +  A + HRLDK TTGL V AK     T+L        +++ Y  +  G   K     +       ++ +M +   +   K  +T YR++E  ++   L ++L TG+ HQIRVHMA I HP+LGD  Y  +
  S:    10 VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVFGGERIEIIVEVEDETR------FEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNAL---LYHYPPISEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLMAV---HPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGR 255
>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 = 264, Expect = 2.6e-21, Identities = 84/272 (30%), Positives = 134/272 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           I KE + + +++F+ +    LS   I  +  +  IKV+      NY ++  + ++I L     KKE + N    K  + ++YED +I+V+NK   ++  P ++    TL N I  Y  E      +   L  RLD  T+GL +  KNQ     L+N   T+   K YL + +G  ++K  T+   I+   E  I  +  E    +E IT Y+VIE      L+E  L TG+ HQIRVH++S+GHP+ GD+ Y  +         L +Y + F
  S:     8 ITKEYDKRKIREFLKEELG-LSSRLIRSAAIDKRIKVDGVSVKMNYVVKTGEEIKIELS----KKESQ-NIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVR--LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVVDER--GQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISRQALHAYGLDF 269
>gi|148240684|ref|YP_001226071.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH 7803] >gi|147849223|emb|CAK24774.1| Pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH 7803] (333 aa)
Score = 264, Expect = 2.6e-21, Identities = 80/256 (31%), Positives = 130/256 (50%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S ++I K I  G ++VN         L++ D +Q+++   P  + L   +L+ + + L+V++ED+++IV+NKP GL   P    K  TL N +   L+   D       L   + HRLDK TTG  V AK+Q+ L +L         S+ YL + +G     S T+   I  +  + K+   +  EN   +   T + + E+  D +LL  +L TG+ HQIRVH A + HPV+GD  Y++      + P    +  +   D
  S:    49 EQSRARIQKFIDAGYVRVNGNTGKAKTPLRQGDEVQLWM---PPPEPLP--YLKPEAMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGL---LHHCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYLAVVHGVPAGDSGTIVGAIGRHPADRKKYAVVSGEN--GRYACTHWSLQERLGDYSLLRFKLDTGRTHQIRVHCAHMNHPVVGDPTYSRCRKLPIELPGQALHAFQLGLD 301
>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 = 264, Expect = 2.7e-21, Identities = 61/182 (33%), Positives = 100/182 (54%)
  Q:    78 EAKP---ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD--KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEE--KQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           EA+P    L+V++ED++++VVNKP G++  P       TL N +  +   +           + HR+DK T+GL V AK       L   +    +++ YL LC G       T++  I  +E   K++  +  ++   K  +T Y+ + + +D AL+E +L TG+ HQ+RVH  SIGHP+LGD  Y +
  S:    80 EAQPQDIKLDVVFEDEHLLVVNKPAGMVVHPAAGNPDGTLVNALLHHCRGQLSGINGVARPGIVHRIDKDTSGLLVVAKTDNAHEGLAAQFAEHTINRRYLALCAGHPNPAEGTIEGRIGRSERDRKKMAPLPEDSSRGKHAVTHYKTLRRLRDCALIECRLETGRTHQVRVHCQSIGHPLLGDPTYGR 268
>gi|194539083|ref|YP_002074143.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25] >gi|151937638|gb|EDN56491.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25] (345 aa)
Score = 264, Expect = 2.7e-21, Identities = 75/277 (27%), Positives = 138/277 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------GNFGFQFPCLTSYKIKFNFDKN 282
           I ++   Q + +F+    K++  S I + ++ G+++VN K+    YKL+  D     +R+ P+  E K + +     LN        +I+ED +++++NKP G         K       I+     +    +LE  L HR+D+ T+G+ + AK +  L  L   +  + V K+YL L  G++K     +   +  NE   I+ ++   K ++   T+++++E+ +   L++   +TG+ HQIRVH    GHP+  D +Y  +      G  G     L +  IKF    N
  S:    44 IDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKAGD----LVRIPPVTVEKKDDDVAPSTKLNKVAELEDMIIFEDDHMLILNKPSGTAVHGGSGLKFGA----IEALRALRPQARFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKKFYLALVMGQWKSSCKVVNAPLLKNEVNSIVRVNPNGKPSE---TRFKILEKFEQATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQHPSN 321
>gi|196195479|gb|EDX90438.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881] (317 aa)
Score = 264, Expect = 2.8e-21, Identities = 78/254 (30%), Positives = 124/254 (48%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN----------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF--LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + I +    Q L +F+    K +  S++ + I++G++++N  +     +L   D     +R+ PI+         A P ++           +YED  + + NKP GL         +  +      Y  EK      E  L HRLD+ T+GL + A+ +  L +L  L     V K Y  LC G FK K  TL   +   +N  ++I+ + RE K +   +T YR++E+     L+E  L TG+ HQIRVH    G P+LGD KY
  S:    14 VTIDEGRHGQRLDNFLFTHLKGVPKSRVYRIIRSGEVRINKGRAKQTTRLASGD----VVRIPPIRTSES----AAPPAVSEGLAERLRRACVYEDDQLFIFNKPSGLAVHGGSGVSLGLIEALRVMYPDEK------EMELVHRLDRDTSGLIMVARRRSFLRKLQRLMQGGQVEKRYWLLCQG-FKGKERTLDAPLLKMMNGNERIVRVSREGKPS---VTHYRLLERFAQAQLVEATLETGRTHQIRVHSQFGGFPLLGDDKY 261
>gi|146306651|ref|YP_001187116.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas mendocina ymp] >gi|145574852|gb|ABP84384.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas mendocina ymp] (332 aa)
Score = 263, Expect = 2.9e-21, Identities = 83/245 (33%), Positives = 134/245 (54%)
  Q:    13 QILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRL------KPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLN-NRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKF---KKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMA-LLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           Q + +F+    K +  + I + ++ G+++VN  +    YKLQ  D +++  LRL      +P+ + L L  LEA     ++YEDK +IV+NKP G+            LN   I+ +   + D   LE  L HRLD+ T+GL + AK +  L  L+     + V K Y+ L  G +   KK+ +       L   ++++E+D E K   E +T +RV+ +  D A L+E + +TG+ HQIRVH    GH + GD+KY
  S:    38 QRIDNFLRTQLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVRVPPLRLAERDEPEPVAQGL-LERLEAA----IVYEDKALIVLNKPAGIAVHGGSG-----LNYGVIEAFRQLRPDAKDLE--LVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMALVRGHWATAKKQVNAPLQKSNLRSGERMVEVDGEGK---EALTLFRVLRRFGDFATLVEAKPVTGRTHQIRVHAKHAGHCIAGDSKY 279
>gi|188159134|ref|ZP_02512193.2| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides LC str. GM12] (302 aa)
Score = 263, Expect = 2.9e-21, Identities = 102/289 (35%), Positives = 174/289 (60%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT-WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLC----HRLDKYTTGLCVAAKNQKTLTELNNLWNT-EAVSKYYLCLCYGKFKKKSDTLKDFIFLNE--------EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF-NFDKNHFLHYLN 289
           M +  + K ++NQ L  F+ K+FK   +S I K I+N  IK+N K+ +  NY L+ ND ++++   KPI ++ + N++ +   L+++YED NI++VNKP  L      N  +D +   +K YL +KK+ + YLE +      HRLDK T+GL + AKN+ + T L N + + + ++KYY  L    +     +L +F+ +N         +K    +D++N + K   T++++I +     L+ ++L+TGKKHQIR  ++   HP+L D +YN K     +   L+++KI+F N +K   L YLN
  S:     1 MTKFVVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRISDKNYLLKINDVIEVYDSNKPIIRD-QFNYI-SNVNLDIVYEDNNILIVNKPNNLEMHSTYNLCLDDM---VKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKSKDQINKYYYALTSSDW-----SLDEFLQVNGYINYDSNIKKADFSLDKKNNY-KYCQTEFKLINKN----LILVKLITGKKHQIRSVLSFYNHPILNDFRYNGKKINDLKMIYLSAFKIEFKNLEKP--LDYLN 288
>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 = 263, Expect = 2.9e-21, Identities = 84/249 (33%), Positives = 128/249 (51%)
  Q:    12 NQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFL-EAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +Q+L D     F E S SK+   I++G++ VN +  T   +K+Q ++       L  ++ E+ +    EA+ I LN++YED++I+V+NKP  L+  P       T+ N +  +  E  DK    A + HRLDK TTGL V AK     T L +      +S+ Y  +  G        +   I  +  K+     RE    K  +T +RVIE+ +    L ++L TG+ HQIRVHMA I HP+LGD  Y  +
  S:    24 DQVLADL----FPEYSRSKLKTWIQDGNVAVNGEVITVPRHKMQMDE-------LVTVQAEMDVQVTSEAQDIALNIVYEDEHILVINKPADLVVHPGAGNPSGTVLNALLNHCPEI-DK-VPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVDQLQRREMSREYEAVALGTMVA-GGIVDAPIGRHATKRTHMAVRE--MGKPAVTHFRVIEKFRAYTHLRLKLETGRTHQIRVHMAHIKHPLLGDQVYGGR 259
>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 = 263, Expect = 3.0e-21, Identities = 84/272 (30%), Positives = 134/272 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           I KE + + +++F+ +    LS   I  +  +  IKV+      NY ++  + ++I L     KKE + N    K  + ++YED +I+V+NK   ++  P ++    TL N I  Y  E      +   L  RLD  T+GL +  KNQ     L+N   T+   K YL + +G  ++K  T+   I+   E  I  +  E    +E IT Y+VIE      L+E  L TG+ HQIRVH++S+GHP+ GD+ Y  +         L +Y + F
  S:     8 ITKEYDKRKIREFLKEELG-LSSRLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELS----KKESQ-NIEPEKMDIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVR--LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVVDER--GQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDEEFISRQALHAYGLDF 269
>gi|88809823|ref|ZP_01125329.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 7805] >gi|88786207|gb|EAR17368.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 7805] (327 aa)
Score = 263, Expect = 3.2e-21, Identities = 79/257 (30%), Positives = 132/257 (51%)
  Q:    24 KELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN--EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           +E S ++I K I  G ++VN +       L++ D +Q+++   P  + L   +L+ + + L+V++ED+++IV+NKP GL   P    K  TL N +   L+   D       L   + HRLDK TTG  V AK+Q+ L +L         S+ YL + +G     S T+   I  +  + K+   +  E+   +   T + + E+  D +LL  +L TG+ HQIRVH A + HPV+GD  Y++      + P    +  +   D
  S:    45 REQSRARIQKFIDAGLVRVNGRTGKAKTPLRQGDEVQLWM---PPPEPLP--YLKPEAMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGL---LHHCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYLAVVHGVPSGDSGTIVGAIGRHPVDRKKYAVVSTES--GRFACTHWSLQERLGDYSLLRFKLDTGRTHQIRVHCAHMNHPVVGDPTYSRCRKLPIELPGQALHAFQLGLD 298
>gi|196193269|gb|EDX88228.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881] (324 aa)
Score = 263, Expect = 3.3e-21, Identities = 78/255 (30%), Positives = 129/255 (50%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKK--KSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +K E   Q +    ++ F   S S++   IKNG + VN  KT    KL  N+SL + + ++P     +L+       L+V+Y+D ++IV+NKP GL+  P       TL N +   L+  +  N L  A + HRLD+ TTGL V A++ +    L      +++ + Y  +  G      K D       ++ +KQ +         K  +T YRV+++ +    +++QL TG+ HQIRVHMA   +P++GD  Y  +
  S:    15 VKPEHAGQRVDQVAAELFDGFSRSRLQTWIKNGVLTVNGAKTKPKEKLTGNESLTLEVEIEP-----ELDDQPQSIDLDVVYQDDDLIVINKPTGLVVHPAAGHADGTLLNGL---LHLDERLNSLPRAGIVHRLDRDTTGLMVVARSLEAHQSLVAQLQDKSLFRQYEAIAVGVMTGGGKVDAPMGRHPVDRKKQAVV----KTGGKNAVTHYRVLDRYRAHTRIQVQLETGRTHQIRVHMAHRNYPLVGDPLYGGR 260
>gi|91977597|ref|YP_570256.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB5] >gi|91684053|gb|ABE40355.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas palustris BisB5] (444 aa)
Score = 263, Expect = 3.3e-21, Identities = 75/254 (29%), Positives = 126/254 (49%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILNV----IYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE--EKQIMEIDRE-NKFNKEIITKYRVIE-QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + +  +E N  +  F+   F  LS S I + ++ G+++VN K+     +L+E  S++I  L+L   K    L+  E K +  +    +YED +++V+NKP GL  Q             I   L   +D    +  L HR+DK T G  + AK +   T L   + + +  K Y  L  G  K K   +  ++  +E  +  IM +    +      +T Y V+E     +A + ++ +TG+ HQ+R HMA IGH ++GD KY
  S:   121 VVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEGQSVRIPPLKLDTPKLPGHLSEAEQKTLQALKEMTLYEDADVLVLNKPLGLAVQGGSGT-----TRHIDLMLEVMRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRSRSARKIYWALVAGVPKPKQGRISTYLAKDESEDDSIMRVAAHGDDGASHAVTYYAVVETSATKLAWVSLKPVTGRTHQLRAHMAHIGHAIIGDPKY 378
>gi|163731255|ref|ZP_02138716.1| ribosomal large subunit pseudouridine synthase C [Vibrio fischeri MJ11] >gi|161395470|gb|EDQ19778.1| ribosomal large subunit pseudouridine synthase C [Vibrio fischeri MJ11] (315 aa)
Score = 263, Expect = 3.4e-21, Identities = 78/265 (29%), Positives = 135/265 (50%)
  Q:    13 QILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIK---------KELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------GNFGFQFPCLTSYKIKF 277
           Q + +F+    K +  S I + ++ G+++VN K+    YKLQE D     +R+ P+K           +KL  + A+    +IYED +++++NKP G         K       I+     + D  +LE  L HR+D+ T+G+ + AK +  L  L   +  + V KYY  L  G++K     +   +  NE   I+ ++   K ++   T+++V+E+ +   L++   +TG+ HQIRVH    GH +  D +Y  +      G FG     L +  IKF
  S:    20 QRIDNFLLARLKNVPKSMIYRIVRKGEVRVNKKRIKPEYKLQEGD----VVRIPPVKVPESTAPDLPNVKLGKV-AELEHCIIYEDDHVLILNKPSGTAVHGGSGLKFGA----IEALRALRPDARFLE--LVHRIDRDTSGILLVAKKRSALRRLQEQFRNKTVQKYYFALVMGQWKNSCKVVNAPLLKNEVNSIVRVNPNGKPSE---TRFKVLEKFEQATLIQASPITGRTHQIRVHTQYTGHSIGWDDRYGDRRFDAYTGQFGLDRLFLHAANIKF 285
>gi|27380477|ref|NP_772006.1| putative ribosomal large subunit pseudouridine synthase C [Bradyrhizobium japonicum USDA 110] >gi|27353641|dbj|BAC50631.1| bll5366 [Bradyrhizobium japonicum USDA 110] (405 aa)
Score = 263, Expect = 3.5e-21, Identities = 74/254 (29%), Positives = 130/254 (51%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILNV----IYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFL--NEEKQIMEIDRE-NKFNKEIITKYRVIEQKKD-MALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + +  +E N  +  F+   F  LS S I + ++ G+++V+ K+     +L+E  S++I  L+L   K   +L+    K +  +    IYED +++V+NKP GL  Q             I + L   +D    +  L HR+DK T+G  + AK +   + L   + + +  K Y  L  G  K K   +  F+    +E+  IM I +  ++     +T Y V+E   + +  + ++ +TG+ HQ+R HM  IGHP++GD KY
  S:    82 VTVTADENNMRVDRFLEARFPGLSFSHIQRVVRKGELRVDGKRVDSKDRLEEGQSVRIPPLKLDAPKAVGELSEAAQKTLKALKEMTIYEDDDVLVLNKPFGLAVQGGSGT-----TRHIDQMLEVMRDSKGQKPRLVHRIDKDTSGCLLIAKTRFAASHLTGAFRSRSARKVYWALVPGLPKPKQGRISTFLAKEESEDDTIMRIAQHGDEGASHAVTYYAVVETAGNKLTWVSLKPVTGRTHQLRAHMEHIGHPIVGDPKY 339
>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 = 262, Expect = 3.9e-21, Identities = 77/242 (31%), Positives = 129/242 (53%)
  Q:    19 ISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKP---ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQ-KKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++  F   S S + K + +G+I VN KK   + K+   D + I +          +  +E +P    L+++YED++II+VNKP+G++  P       TL N +   +Y  KD        L   + HR+D  TTGL V  KN      L+      ++++ Y  +C+  F +    +   I  +  +++ M ++ +N  N   +T Y+V+++ K +  L+E QL TG+ HQIRVHM+ I HP+LGD  Y  K
  S:    21 LADYFDNYSRSFLKKLLDDGNILVNDKKAKPSLKIASGDRIDITIP--------SIASVEIEPENIPLDIVYEDEDIIIVNKPKGMVVHPAPGHYSGTLVNGL---MYHFKDSLSGINGELRPGIVHRIDMDTTGLLVVCKNDAAHNFLSEQLAVHSITRKYYAICFNYFTEDEGIVDLPIGRHPTDRKKMAVNYKNGRNA--VTHYKVLKKLKNNFCLIECQLETGRTHQIRVHMSYIKHPLLGDAIYGPK 259
>gi|156975190|ref|YP_001446096.1| rRNA ribosomal pseudouridine synthase [Vibrio harveyi ATCC BAA-1116] >gi|156526784|gb|ABU71870.1| hypothetical protein VIBHAR_02917 [Vibrio harveyi ATCC BAA-1116] (339 aa)
Score = 262, Expect = 4.0e-21, Identities = 76/277 (27%), Positives = 137/277 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------GNFGFQFPCLTSYKIKFNFDKN 282
           I ++   Q + +F+    K++  S I + ++ G+++VN K+    YKL+  D     +R+ P+  E K + +     LN        +I+ED +++V+NKP G         K       I+     +    +LE  L HR+D+ T+G+ + AK +  L  L   +  + V K+Y  L  G++K     +   +  NE   I+ ++   K ++   T+++V+E+ +   L++   +TG+ HQIRVH    GHP+  D +Y  +      G  G     L +  IKF    N
  S:    38 IDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKAGD----LVRIPPVTVEKKEDDVAPSTKLNKVAELEHMIIFEDDHMLVLNKPSGTAVHGGSGLKFGA----IEALRALRPQARFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKKFYFALVMGEWKNSCKVVNAPLLKNEVNSIVRVNPNGKPSE---TRFKVLERFEQATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQHPSN 315
>gi|86749455|ref|YP_485951.1| pseudouridine synthase RluD [Rhodopseudomonas palustris HaA2] >gi|86572483|gb|ABD07040.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas palustris HaA2] (453 aa)
Score = 262, Expect = 4.0e-21, Identities = 75/254 (29%), Positives = 127/254 (50%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILNV----IYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFL--NEEKQIMEI-DRENKFNKEIITKYRVIE-QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + +  +E    +  F+   F  LS S I + ++ G+++VN K+     +L+E  S++I  L+L   K    L+  E K +  +    +YED +++V+NKP GL  Q             I   L   +D    +  L HR+DK T G  + AK +   T L   +   +  K Y  L  G  K K   +  ++    +E+  IM I +  ++     +T Y V+E   + +A + ++ +TG+ HQ+R HMA IGH ++GD KY
  S:   130 VVVTADENGMRVDRFLEGRFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEGQSVRIPPLKLDTPKAPGHLSEAEQKTLAALKAMTLYEDADVLVLNKPAGLAVQGGSGT-----TKHIDLMLEVMRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHRSARKIYWALVAGVPKPKQGRISTYLAKEESEDDSIMRIAEHGDEGASHAVTYYAVVETSAQKLAWVSLKPVTGRTHQLRAHMAHIGHAIVGDPKY 387
>gi|71907236|ref|YP_284823.1| ribosomal large subunit pseudouridine synthase D [Dechloromonas aromatica RCB] >gi|71846857|gb|AAZ46353.1| ribosomal large subunit pseudouridine synthase D [Dechloromonas aromatica RCB] (318 aa)
Score = 262, Expect = 4.0e-21, Identities = 67/186 (36%), Positives = 99/186 (53%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           L+V++ED+ ++V+NKP GL+  P       TL N +  ++     +    A + HRLDK T+GL V AK  +  T+L        V + YL L  G  K +  T+ + I  +  ++I M I  EN+  K  IT  R++E       +E  L TG+ HQIRVHMA+I HP++GD  Y K      +FP
  S:    95 LDVVFEDETLLVINKPAGLVVHPGSGNWSGTLMNALLHHV--PGIEVVPRAGIVHRLDKDTSGLLVVAKTLEAQTDLVRQLQARTVRRIYLALAAGAMKHEG-TVNEPIGRHPSQRIKMAIVPENRGGKPAITNIRILEAFTYTTFVECSLETGRTHQIRVHMAAIHHPLVGDQVYGKHNPKLPEFP 278
>gi|161507179|ref|YP_001577133.1| ribosomal large subunit pseudouridine synthase [Lactobacillus helveticus DPC 4571] >gi|160348168|gb|ABX26842.1| ribosomal large subunit pseudouridine synthase [Lactobacillus helveticus DPC 4571] (298 aa)
Score = 262, Expect = 4.1e-21, Identities = 86/262 (32%), Positives = 142/262 (54%)
  Q:     5 FIKKEEENQILKDFISKS-FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLE-AKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQ 266
            + +E++ + L  F+ K+ F   +L K      +G I VNHK+   ++ L   D + IF+      +E K  FL+ +   ++ ++E KN IV+NKP G++  P + E  D + NR+  Y  ++  K+ L+ ++  RLD+ T+GL +  KN       + +     V KY+  + +G F +  D L   I     K+   + R    N K+  T+YRV++Q +  +L+E++LLTG+ HQIRVHMA +GHP+ GD  Y    NF  Q
  S:     7 LVVQEKDPKKLGSFLLKNGFSHQALIKARH--HHGMILVNHKRRYLSFHLSAGDEV-IFVS----GEEKKNQFLKPSNNPVDPVFETKNYIVLNKPAGVLSIPSRYEDNDAVVNRLMGYFLQQNKKD-LKPHVITRLDRDTSGLVLVGKNAIAHARFSKIGKDNFVKKYH-AIVHGNFAE--DELTGIIDEPIGKEGDGVKRAVVANGKKAQTRYRVLKQVEGASLVELRLLTGRTHQIRVHMAYLGHPLFGDPLYGINDNFSRQ 260
>gi|16272141|ref|NP_438344.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae Rd KW20] >gi|1175998|sp|P44445|RLUD_HAEIN Ribosomal large subunit pseudouridine synthase D (rRNA-uridine isomerase D) (rRNA pseudouridylate synthase D) >gi|1573131|gb|AAC21845.1| sfhB protein (sfhB) [Haemophilus influenzae Rd KW20] (324 aa)
Score = 262, Expect = 4.1e-21, Identities = 76/255 (29%), Positives = 127/255 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++ E+  Q L   +++ F E S S++   I+   +K+N + T     K+   + ++I + ++   +       EA+ I LN++YED +IIV+NKP+ L+  P       T+ N +   LY          A + HRLDK TTGL V AK     T+L        +++ Y  +  G   K     +       ++ +M +   +   K  +T YR++E  ++   L ++L TG+ HQIRVHMA I HP+LGD  Y  +
  S:    10 VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVEVEDETR------FEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNAL---LYHYPPIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLMAV---HPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGR 255
>gi|119503335|ref|ZP_01625419.1| ribosomal large subunit pseudouridine synthase C [marine gamma proteobacterium HTCC2080] >gi|119460981|gb|EAW42072.1| ribosomal large subunit pseudouridine synthase C [marine gamma proteobacterium HTCC2080] (320 aa)
Score = 262, Expect = 4.1e-21, Identities = 71/249 (28%), Positives = 129/249 (51%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKF----KKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           EE  Q L +F+ +    +  ++I ++I+ G+++V+  +   + +L+   S++I  LR+    +         +   ++I E+  ++VVNKP GL         +  +     + +YE     YLE  L HRLD+ T+GL + A+   TL  L+ L  +  + K YLCL  G++    K+    L+ F   + E+++    +     ++ +T +RV+ +     L+E + +TG+ HQIRVH    G P+LGD KY
  S:    26 EEAGQRLDNFLQRVRGGVPKTRIYRAIRKGEVRVDKGRVKPDTRLEAGVSVRIPPLRVPEKAEAAGAAGWRTRLRASIIREESTLLVVNKPPGLAVHGGSGINVGLIETL--RAMYETD--RYLE--LVHRLDRDTSGLLLVARRASTLRNLHVLLRSNGIDKRYLCLVNGRWPAHLKRVDAPLEKFALPSGERRV----KVAATGRQSLTTFRVVRRWSSATLVEAKPVTGRTHQIRVHCQHAGFPILGDAKY 269
>gi|118727962|ref|ZP_01576543.1| pseudouridine synthase [Clostridium cellulolyticum H10] >gi|118662648|gb|EAV69328.1| pseudouridine synthase [Clostridium cellulolyticum H10] (223 aa)
Score = 262, Expect = 4.2e-21, Identities = 65/180 (36%), Positives = 107/180 (59%)
  Q:    82 ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY----NKKG 261
           I  ++YED +++VV KP  +  Q D ++ ID L   +K+YL EK +K   +   L HRLD+   G+ V AK  K  + L++   T    K YL +  G  +K+ D L++F+  +  + ++ + +E   + KE I  Y V++   +++LL+IQL TG+ HQIRV ++  G+P+ GD +Y    NK G
  S:     2 IPKIVYEDNHLLVVEKPVNIPVQADNSKDIDMLT-LLKQYLKEKYNKPGEVYLGLVHRLDRPVGGVMVFAKTSKCASRLSDQIRTRTFKKTYLAIVRGVPQKQKDELRNFLLKDSSENMVHVVKEGTRDAKEAILDYEVLKSNGELSLLQIQLHTGRPHQIRVQLSHSGYPLYGDQRYGIYVNKPG 186
>gi|119470041|ref|ZP_01612846.1| 23S rRNA pseudouridine synthase [Alteromonadales bacterium TW-7] >gi|119446751|gb|EAW28024.1| 23S rRNA pseudouridine synthase [Alteromonadales bacterium TW-7] (325 aa)
Score = 262, Expect = 4.3e-21, Identities = 86/260 (33%), Positives = 127/260 (48%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHK-KTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-NYLEANLCHRLDKYTTGLCVAAKNQKTLTEL-NNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN-----KKGNFGFQFPCLTSYK 274
           L   +++ F + S S+I   I +  I V+ +   T   KL   + L +   ++  ++ L  N       LN++YED +I+V+NKP GL+  P       T+ N +   L+   D  N   A + HRLDK TTGL V AK  +  T L   L   E  ++ Y  LC G         K       ++  M +   ++  K  IT YRV E+ +    L ++L TG+ HQIRVHMA + HP++GD  YN      KG     F  L S+K
  S:    20 LDQVLAQLFPDYSRSRIKTWILDDKITVDGEILNTPRTKLLGGEVLNVETTIEAPREYLAQNI-----DLNIVYEDDHILVINKPMGLVVHPGAGNPDGTVLNAL---LHHYPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTHLVKALQKRENFTREYEALCNGTMTAGGMVEKPIGRHATQRTHMAV---HEMGKPAITHYRVAEKFRAHTRLRLRLETGRTHQIRVHMAYLNHPLIGDQSYNGRPRPPKGATPQLFELLRSFK 276
>gi|167764292|ref|ZP_02436419.1| hypothetical protein BACSTE_02677 [Bacteroides stercoris ATCC 43183] >gi|167698408|gb|EDS14987.1| hypothetical protein BACSTE_02677 [Bacteroides stercoris ATCC 43183] (356 aa)
Score = 262, Expect = 4.4e-21, Identities = 74/255 (29%), Positives = 123/255 (48%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE--KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++ + K +E   +  ++       S ++I K+   G +  N K    +YK++  D + + +     + E+     E  P L+++YEDK ++VVNKP GL+  P       TL N I  ++ +    D N     L HR+DK T+GL V AK     T L   +  +   + Y  L +G   +   T+   +  N + ++      +   K  +T YRV+E+   + L+E  L TG+ HQIRVHM  IGH +  D +Y
  S:    31 RVVVDKGQEMVRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKSSYKVKPLDVITVMMDRPRYENEV---IPEDIP-LDIVYEDKYLMVVNKPAGLVVHPGHGNYRGTLVNAIAWHMKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGNVGQDEGTIVGNVGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMKHIGHILFNDERY 283
>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 = 262, Expect = 4.5e-21, Identities = 75/256 (29%), Positives = 122/256 (47%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           +K  +  Q L   +++ F + S S++ + +  G I VN    T    K+   + + +   L+  ++       EA+ + LN++YED +IIV+NKPR  +  P   +   T+ N +    +         A + HRLDK TTGL V AK     T L        V++ Y  +  G         K     + ++ +M +   +   K  +T YRV E  ++   L ++L TG+ HQIRVHMA + HP+LGDT Y  + 
  S:    11 VKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQAELEDEQR------WEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNAL--LFHYSPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMTAGGMIDKPIGRHSTKRTLMSV---SPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRA 257
>gi|162447506|ref|YP_001620638.1| pseudouridylate synthase, 23S RNA-specific [Acholeplasma laidlawii PG-8A] >gi|161985613|gb|ABX81262.1| pseudouridylate synthase, 23S RNA-specific [Acholeplasma laidlawii PG-8A] (277 aa)
Score = 262, Expect = 4.6e-21, Identities = 78/227 (34%), Positives = 119/227 (52%)
  Q:    31 ISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL-YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I K   N   +VN K     Y+L++ D L I L      +   +N +E    L++IYED +I++VNKP  +I   D   + D L  R+  +  Y       L A   HR+DK TTG+ V AK+   L  L+NL+ +  V K Y+C+   K K K+ +++  +  + + Q M +    K     IT Y ++  +   + L++Q+ TG+ HQIR HMASI HPV+GD  Y
  S:    31 IYKYSSNHLFEVNFKAVNSEYRLKKGDVLNIHL------EPYVMNDIEDVE-LDIIYEDDDIVIVNKPFNVIVHDDGASE-DHLTRRVNMHFQYHGYHHQVLPA---HRIDKETTGIVVFAKHFIALAYLSNLFESRQVVKNYICVVENKVKDKTGSIESKLIKDSKLQKMVVSPHGKL---AITHYELLGYEATRSRLKVQIETGRTHQIRAHMASINHPVVGDILY 244
>gi|77460386|ref|YP_349893.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas fluorescens PfO-1] >gi|77384389|gb|ABA75902.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas fluorescens PfO-1] (320 aa)
Score = 262, Expect = 4.6e-21, Identities = 79/252 (31%), Positives = 132/252 (52%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELK----------LNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLN-NRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFI---FLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMA-LLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +  E   Q + +F+    K +  + I + ++ G+++VN  +    YKLQ  D     +R+ P++   +          L  LEA    +++YEDK +IV+NKP G+            LN   I+ +   + D   LE  L HRLD+ T+GL + AK +  L  L+     + V K Y+ L  G +      ++  +    L   ++++E+D E    KE +T ++V+ +  D A L+E + +TG+ HQIRVH    GH + GDTKY
  S:    16 VSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGD----IVRVPPVRVPERDEPVPLAQGLLQRLEA----SIVYEDKALIVINKPAGIAVHGGSG-----LNYGVIEAFRQLRPDAKELE--LVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYMALVRGNWATSIKQVRAALGKSNLRSGERMVEVDEEE--GKESVTVFKVLRRFGDFATLIEAKPITGRTHQIRVHTLHAGHCIAGDTKY 265
>gi|39936271|ref|NP_948547.1| pseudouridine synthase RluD [Rhodopseudomonas palustris CGA009] >gi|39650126|emb|CAE28649.1| possible ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas palustris CGA009] (455 aa)
Score = 262, Expect = 4.7e-21, Identities = 74/254 (29%), Positives = 127/254 (50%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILNV----IYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE--EKQIMEIDRE-NKFNKEIITKYRVIEQK-KDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + +  +E    +  F+   F  LS S I + ++ G+++VN K+     +L+E  S++I  L+L   K    L+  E K +  +    ++ED +++V+NKP GL  Q             I + L   +D    +  L HR+DK T G  + AK +   T L   +   +  K Y  L  G  K K   +  ++  +E  E  IM + +  +      +T Y V+E   + +A + ++ +TG+ HQ+R HMA IGH ++GD KY
  S:   132 VTVTADENGMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEGQSVRIPPLKLDTPKLPGHLSEAEQKTLQTLKAMTLFEDADVLVLNKPAGLAVQGGSGT-----TRHIDQMLEVLRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHRSARKIYWALVAGVPKPKQGRISTYLAKDESEEDSIMRVAKHGDDGASHAVTYYAVVETSGQKLAWVSLKPVTGRTHQLRAHMAHIGHAIVGDPKY 389
>gi|169634491|ref|YP_001708227.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii SDF] >gi|169153283|emb|CAP02389.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii] (310 aa)
Score = 262, Expect = 4.8e-21, Identities = 77/252 (30%), Positives = 130/252 (51%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN---------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF----LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + + +  Q + +F+    K +  S+I + I+ G ++VN K+     KL   D +    R+ PI+ E K     A P+ +         V+YED+ ++VVNKP G+            +     + L     K YLE  L HR+D+ T+GL + +K + TL  L ++     + K Y  +  G+       +   +F     N E+++  + +E K +K   T++ V E+ K+  L+    L+G+ HQIRVH  SIGHP++GD KY
  S:    15 VDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQI----RVAPIRYEQKDE--TAAPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGVAYGLI-----EALRAATGKKYLE--LIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAIVKGQVSLDKQLIDAPLFRYELANGERRV-RVSKEGKPSK---TEWVVAERFKNATLVHASPLSGRTHQIRVHGLSIGHPLVGDDKY 262
>gi|134095276|ref|YP_001100351.1| 23S rRNA pseudouridylate synthase [Herminiimonas arsenicoxydans] >gi|133739179|emb|CAL62228.1| Ribosomal large subunit pseudouridine synthase C (rRNA-uridine isomerase C) (rRNA pseudouridylate synthase C) [Herminiimonas arsenicoxydans] (326 aa)
Score = 262, Expect = 4.8e-21, Identities = 76/260 (29%), Positives = 129/260 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLK----DFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGF 265
           I +EE  Q + +F+ +  K +  S I + +++G+++VN  +    Y+L E D     +R+ PI+   K           ++ ED +++V++KP G+                I++    + D  +LE  L HRLD+ T+G+ V AK +  LT L+         K YL L +G +K     +K     +   + E+++    R      E  T + +I++  + ALLE +L TG+ HQIRVH+AS G  + GD KY   G+F  
  S:    23 ISEEEAGQRIDNFLLRICKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLTEGD----VVRIPPIRIAEKAPSTAPGAEFKILLEDNHLLVIDKPAGVAVHGGSGVSYGV----IEQLRAARPDAKFLE--LVHRLDRDTSGVLVLAKKRSALTNLHEQIRGGEPDKRYLVLVHGDWKNARQHIKLALHKYSTADGERRV----RVQADGMESHTIFNLIQRYGEFALLEAELKTGRTHQIRVHLASSGFAIAGDDKY---GDFAL 269
>gi|196248006|ref|ZP_03146708.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16] >gi|196212790|gb|EDY07547.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16] (299 aa)
Score = 262, Expect = 4.8e-21, Identities = 73/252 (28%), Positives = 131/252 (51%)
  Q:     6 IKKEEENQILKDFISKS-FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTL-NNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I ++ + ++L+ F+ ++     +L+ I      G + VN +  T  + L+  ++L +     P ++       EA P L+++YED+ ++VVNKP GL   P ++    TL N  +  Y  ++ D      ++  RLD+ T+GL + AK++     L+ L     V++ Y  +C+G   ++  T+   I    +  I    RE+   K  IT +RV+E+      + ++L TG+ HQIRVH+A +GHP+ GD  Y
  S:    10 INEQHDGKLLRQFLQENGISRTALTDIK--FHGGALYVNSRPVTVRHVLRAGETLSVVF---PPERTSDWMDPEAMP-LDIVYEDEYVLVVNKPAGLATIPSRHHPGGTLANGLLHHYRQQQLDST---VHIITRLDRDTSGLVLVAKHRHVHHLLSTLQQKGQVTRTYEAVCHGVIDEEEGTIDAPIGRQNDSIIAREVRED--GKRAITHFRVLERLSGYTYVSLRLETGRTHQIRVHLAYLGHPLAGDELY 252
>gi|53733124|ref|ZP_00156017.2| COG0564: Pseudouridylate synthases, 23S RNA-specific [Haemophilus influenzae R2866] >gi|145639768|ref|ZP_01795370.1| SfhB [Haemophilus influenzae PittII] >gi|145271136|gb|EDK11051.1| SfhB [Haemophilus influenzae PittII] (324 aa)
Score = 261, Expect = 5.2e-21, Identities = 76/255 (29%), Positives = 127/255 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++ E+  Q L   +++ F E S S++   I+   +K+N + T     K+   + ++I + ++   +       EA+ I LN++YED +IIV+NKP+ L+  P       T+ N +   LY          A + HRLDK TTGL V AK     T+L        +++ Y  +  G   K     +       ++ +M +   +   K  +T YR++E  ++   L ++L TG+ HQIRVHMA I HP+LGD  Y  +
  S:    10 VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVEVEDETR------FEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNAL---LYHYPPIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLMAV---HPIGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGR 255
>gi|118580263|ref|YP_901513.1| pseudouridine synthase [Pelobacter propionicus DSM 2379] >gi|118502973|gb|ABK99455.1| pseudouridine synthase [Pelobacter propionicus DSM 2379] (238 aa)
Score = 261, Expect = 5.4e-21, Identities = 55/175 (31%), Positives = 102/175 (58%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           L V+YED++II++ KP GL+      +K  T+++ +  Y+ +   ++     + HRLD+ T+G+ + AK++     L   W  +   K+Y+ + +G    KS T+  ++  N   ++     + +  K   T+Y V+++ + ++LL I LLTG+KHQIRVH++  G+ V+GD+KY
  S:    11 LTVLYEDRDIIIIEKPCGLLTIGTGRDKTRTVHSILNDYVRKGDPRSRNRVYIVHRLDRETSGILILAKSEANKIYLQEHW--QETDKHYVAVVHGTLALKSGTISSYLAENSAMRVYSTTDQAQ-GKLSHTEYVVMKENRGLSLLAIHLLTGRKHQIRVHLSEGGNAVVGDSKY 182
>gi|192810312|ref|ZP_03038985.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC10] >gi|192800604|gb|EDV77111.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC10] (354 aa)
Score = 261, Expect = 5.5e-21, Identities = 78/256 (30%), Positives = 135/256 (52%)
  Q:     2 IQIFIKKEEENQILKDFISK----SFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRE--NKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I+  +   E+  +LK  + K    S K LS  K+++      I +N  +   + K+Q  D ++I +      ++ + N +  +P+ L+++YED++++V+NKP G+I  P      DTL N +  Y +++K  NY      HRLD+ T+G+ V AKN      ++       V K Y+   +G+   ++  +   I    ++  +E  R          +T+YRV E     +L+E++L TG+ HQIRVHM SIG P++GD  Y
  S:     8 IRYVVPSHEDGMLLKTILQKRMGVSRKLLSRLKLTEQ----GIMLNGTRVYISVKVQAGDLVEIRM------EQERSNDMLPQPMELHILYEDEHLLVLNKPAGVIVHPTHGHYTDTLANGVVHY-WQEKGWNY-RFRAVHRLDQETSGVLVIAKNAYIHQHVSEQMIAGTVDKRYVAFVHGRPSSQTGDIDGPI----DRDPLEPHRRIVTPEGYPSLTRYRVCETYPSASLVELKLETGRTHQIRVHMLSIGCPLIGDQMY 254
>gi|110833337|ref|YP_692196.1| pseudouridylate synthase [Alcanivorax borkumensis SK2] >gi|110646448|emb|CAL15924.1| pseudouridylate synthase [Alcanivorax borkumensis SK2] (323 aa)
Score = 261, Expect = 5.5e-21, Identities = 77/255 (30%), Positives = 130/255 (50%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKK--KSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           +K E   Q +    ++ F+  S S++   IKNG + VN  +T    KL  N+SL + + ++P     +L+       L+V+Y+D ++IV+NKP GL+  P       TL N +   L+  +  N L  A + HRLD+ TTGL V A++ +    L      +++ + Y  +  G      K D       ++ +KQ +         K  +T YRV+++ +    +++QL TG+ HQIRVHMA   +P++GD  Y  +
  S:    15 VKPEHAGQRVDQVAAELFEGFSRSRLQTWIKNGVLTVNGAQTKPKEKLTGNESLTLEVEIEP-----ELDDQPQSIDLDVVYQDDDLIVINKPTGLVVHPAAGHADGTLLNGL---LHLDERLNSLPRAGIVHRLDRDTTGLMVVARSLEAHQSLVAQLQDKSLFRQYEAIAVGVMTGGGKVDAPMGRHPVDRKKQAVV----KTGGKNAVTHYRVLDRYRAHTRIQVQLETGRTHQIRVHMAHRNYPLVGDPLYGGR 260
>gi|42518750|ref|NP_964680.1| hypothetical protein LJ0825 [Lactobacillus johnsonii NCC 533] >gi|41583036|gb|AAS08646.1| hypothetical protein LJ_0825 [Lactobacillus johnsonii NCC 533] (299 aa)
Score = 261, Expect = 5.5e-21, Identities = 78/241 (32%), Positives = 130/241 (53%)
  Q:    38 GDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFK--KKSDTLKDFIFLNEEKQIMEIDRENKFN-----KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFN 278
           G + VNH +   +Y L   D +   L  +   K LK     +   LN+++E K+ +V+NK  G++  P + E  D + NR+  Y  ++K  + L+ ++  RLD+ T+GL +  KN       + +   E + KY+  + +G F+  ++  T+        +  I +ID   K       +  +TKYRV++Q K  +L+E+QLLTG+ HQIRVHM  +GHP+ GD  Y  K NF  Q   L  + ++F+
  S:    38 GMVLVNHHRRYTSYLLHAGDEVIFILGEEKENKWLK----PSSKKLNIVFEQKDYLVINKDAGILSIPSRYEDSDAVVNRLLHYFQQQKQTD-LKPHVITRLDRDTSGLVLVGKNAVAHARFSKMEKNEFIKKYH-AIVHGNFEEAQRQGTI--------DAPIGKIDAGVKRGVVNNGQRSVTKYRVLDQVKGASLIELQLLTGRTHQIRVHMQYLGHPLFGDPLYGIKDNFKRQ--ALNCFYLEFD 269
>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 = 261, Expect = 5.7e-21, Identities = 75/256 (29%), Positives = 122/256 (47%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTW-NYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           +K  +  Q L   +++ F + S S++ + +  G I VN    T    K+   + + +   L+  ++       EA+ + LN++YED +IIV+NKPR  +  P   +   T+ N +    +         A + HRLDK TTGL V AK     T L        V++ Y  +  G         K     + ++ +M +   +   K  +T YRV E  ++   L ++L TG+ HQIRVHMA + HP+LGDT Y  + 
  S:    11 VKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQAELEDEQR------WEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNAL--LFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMTAGGMIDKPIGRHSTKRTLMSV---SPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRA 257
>gi|53804453|ref|YP_113936.1| ribosomal large subunit pseudouridine synthase C [Methylococcus capsulatus str. Bath] >gi|53758214|gb|AAU92505.1| ribosomal large subunit pseudouridine synthase C [Methylococcus capsulatus str. Bath] (316 aa)
Score = 261, Expect = 5.8e-21, Identities = 72/254 (28%), Positives = 133/254 (52%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKE-LKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF---LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I +  E   Q + +F+    K +  S + + ++ G +++N  ++    +L E D ++I  LRL    +  +   +LE +    +++ED++++VVNKP G+        +       I+     ++D  +LE  L HRLD+ T+G  + AK +  L +L+  +  E V K YL L  G + ++   +   +    L   +++++I  E K     IT++R +E      L+E + +TG+ HQIRVH  S+GHP+ GD +Y
  S:    15 IEVDAETAGQRIDNFLFSRLKGVPKSHVYRILRTGQVRINGGRSKAQQRLNEGDVVRIPPLRLAEAPEAGIPTPWLENR----ILHEDEDLLVVNKPAGMAVHGGSGLRFGV----IEGLRAAREDARFLE--LVHRLDRDTSGCLLIAKRRSALRQLHEQFRGEGVDKTYLALFSGVWARRRQVVDAPLLKNVLQSGERMVKISSEGK---AAITEFRRLEPLSGATLVEARPVTGRTHQIRVHARSLGHPLAGDERY 260
>gi|186457897|ref|ZP_02968207.1| pseudouridine synthase [bacterium Ellin514] >gi|184205552|gb|EDU02601.1| pseudouridine synthase [bacterium Ellin514] (260 aa)
Score = 261, Expect = 6.2e-21, Identities = 56/184 (30%), Positives = 101/184 (54%)
  Q:    74 LNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI----MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           LN +E   + +V++ED  ++V+NKP GL+C P K ++  +L +R++ +L  +        +L +RLD+ T+G+ + AK+  T   L  +W    V K YL + +G  +++  T++  +  +    I      ++       +   K R   ++ D  LL +   TG+KHQIR+H+A I HP++GD  Y
  S:    19 LNKMEK--LFDVVHEDAELLVINKPAGLVCHPTKGDEYSSLISRVRLHLGPES-----HPHLVNRLDRETSGIVIVAKDDTTARGLRRIWEGREVQKEYLAIVHGHVREEQGTIQAALGKDTSSIIAIKDTVVEGGAASQTDFTVKKRFSREEGDFTLLRVLPHTGRKHQIRIHLAHIDHPIVGDKMY 199
>gi|104783634|ref|YP_610132.1| 23S rRNA pseudouridine synthase [Pseudomonas entomophila L48] >gi|95112621|emb|CAK17349.1| 23S rRNA pseudouridine synthase [Pseudomonas entomophila L48] (320 aa)
Score = 261, Expect = 6.3e-21, Identities = 78/252 (30%), Positives = 125/252 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI--FLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +  E   Q L    ++ F E S S++S  IK+G + V+         L+  D++     L L+  ++E +  ++     L+++YED  I+V+NKP GL+  P       TL N +   L+   D  N   A + HRLDK TTGL V AK  +  T L +     +VS+ Y C+  G                 E+Q M +       K  ++ YRV+++ +    + ++L TG+ HQIRVHMA +G+P++GD  Y
  S:    11 VPSELGGQRLDQVAAQLFSEYSRSRLSSWIKDGRLTVD------GAVLRPRDTVHSGSILALEA-EQEAQGEWVAQDIELDIVYEDDQILVINKPAGLVVHPAAGHPDGTLLNAL---LHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTLQAQTNLVDQLQKRSVSRIYECIVVGVVIAGGKIDAPIGRHGGERQRMAV---TDGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGYPLVGDQTY 252
>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 = 260, Expect = 6.6e-21, Identities = 77/235 (32%), Positives = 121/235 (51%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRE------NKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNK 259
           E S ++I K I++G + VN  +      L+  D +Q++     +     L +L+ + + L++I+ED +IIV+NKP GL   P    K  TL N +  +  +    N  L   + HRLDK TTG  V AK+Q+ L  L         S+ Y+ L +G        +   I  +       IDR+      +   ++  T + + E+  D +LL  +L TG+ HQIRVH A IGHP+LGD  Y++
  S:    39 EQSRARIQKFIEDGLVLVNGIQGKSKTPLRTGDEIQLW-----VPPPEPLPYLKPQKMHLDIIFEDSHIIVINKPAGLTVHPAPGNKDRTLVNGLLHHCTDLPGINGKLRPGIVHRLDKDTTGCIVIAKSQEALVNLQVQIQKRIASRRYIALVHGVPHGDKGIISAPIGRHP------IDRKKYAVVNDGSGRDACTHWELKERLGDYSLLSFKLETGRTHQIRVHSAHIGHPILGDPTYSR 270
>gi|108757849|ref|YP_631549.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622] >gi|108461729|gb|ABF86914.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622] (346 aa)
Score = 260, Expect = 6.8e-21, Identities = 77/249 (30%), Positives = 131/249 (52%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYG--KFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           E   + +  +++++F +L+ S+I   I+ G +  + +      +L+  + L +      I   +    L  +  L +++ED++++VV+K  G++  P       TL N +   L+  KD       L   + HRLDK TTG  V AKN++ L  L   + T AV K YL L +G    + + +TL     ++ ++   ++    K  K  IT+YRV+E     AL+E+ LLTG+ HQIRVH++  GHP+L D  Y
  S:    14 EARGERVDQYLARAFPDLTRSRIHGLIEAGHVLADGQPAKPARRLRGGELLVLH-----IPAPVPAVPLAEELPLALLHEDRDLVVVDKAAGMVVHPGAGHASGTLVNAL---LHRVKDLAGVGGELRPGIVHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLALVHGVPPAEGRIETLYGRHPIHRQRFTGKV----KEGKNAITEYRVLETFDGAALVEVDLLTGRTHQIRVHLSEAGHPLLCDALY 256
>gi|164686622|ref|ZP_02210650.1| hypothetical protein CLOBAR_00215 [Clostridium bartlettii DSM 16795] >gi|164604351|gb|EDQ97816.1| hypothetical protein CLOBAR_00215 [Clostridium bartlettii DSM 16795] (221 aa)
Score = 260, Expect = 7.0e-21, Identities = 71/195 (36%), Positives = 111/195 (56%)
  Q:    82 ILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEI-DRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIK 276
           +LNVIYED +++VV KP  ++ Q D N   D + N +KKYL EK +K   +   L HRLD+   G+ V AK  K  + L+     +   K Y  + +G+ KKK D L D+++ +++  ++ + ++ +K  K+    Y+ +      +L+EI L TG+ HQIRV  +S  HP+ GD +Y K  N   Q   L SYKI+
  S:     1 MLNVIYEDNHLLVVEKPVNILSQGD-NTNDDDMVNLLKKYLKEKYNKPGNVFVGLVHRLDRPVGGIMVFAKTSKAASRLSEQVRNKTFKKTYKAVLHGEMKKKQDNLSDYLYKDKKTNMVSVVNKNHKDAKDAKLSYKTLASNNGFSLVEIDLQTGRPHQIRVQFSSRNHPLYGDQRYGKNVNKKGQQIALWSYKIE 196
>gi|42561291|ref|NP_975742.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides SC str. PG1] >gi|42492789|emb|CAE77384.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides SC str. PG1] (302 aa)
Score = 260, Expect = 7.0e-21, Identities = 102/289 (35%), Positives = 172/289 (59%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTT-WNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLC----HRLDKYTTGLCVAAKNQKTLTELNNLWN-TEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI----MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF-NFDKNHFLHYLN 289
           M +  + K ++NQ L  F+ K+FK   +S I K I+N  IK+N K+ +  NY L+ ND ++++   KPI ++ + N++ +   L++IYED NI++VNKP  L      N  +D +   +K YL +KK+ + YLE +      HRLDK T+GL + AKN+ + T L N +   + ++KYY  L    +    + L+   ++N +  I      +D++N + K   T++++I +     L+ ++L+TGKKHQIR  ++   HP+L D +YN K     +   L+++KI+F N +K   L YLN
  S:     1 MTKFVVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRISDKNYLLKVNDIIEVYDSNKPIIRD-QFNYI-SNVNLDIIYEDNNILIVNKPNNLEMHSTYNLCLDDM---VKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKLKDQINKYYYALTSCDWNL-DEFLQVNGYINYDSNIKRAHFSLDQKNNY-KYCQTEFKLINKN----LILVKLITGKKHQIRSVLSFYNHPILNDFRYNGKKINDLKMIYLSAFKIEFKNLEKP--LDYLN 288
>gi|27804835|gb|AAO22876.1| AgmF [Myxococcus xanthus] (264 aa)
Score = 260, Expect = 7.1e-21, Identities = 77/249 (30%), Positives = 131/249 (52%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYG--KFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           E   + +  +++++F +L+ S+I   I+ G +  + +      +L+  + L +      I   +    L  +  L +++ED++++VV+K  G++  P       TL N +   L+  KD       L   + HRLDK TTG  V AKN++ L  L   + T AV K YL L +G    + + +TL     ++ ++   ++    K  K  IT+YRV+E     AL+E+ LLTG+ HQIRVH++  GHP+L D  Y
  S:    14 EARGERVDQYLARAFPDLTRSRIHGLIEAGHVLADGQPAKPARRLRGGELLVLH-----IPAPVPAVPLAEELPLALLHEDRDLVVVDKAAGMVVHPGAGHASGTLVNAL---LHRVKDLAGVGGELRPGIVHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLALVHGVPPAEGRIETLYGRHPIHRQRFTGKV----KEGKNAITEYRVLETFDGAALVEVDLLTGRTHQIRVHLSEAGHPLLCDALY 256
>gi|70732611|ref|YP_262374.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas fluorescens Pf-5] >gi|68346910|gb|AAY94516.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas fluorescens Pf-5] (353 aa)
Score = 260, Expect = 7.3e-21, Identities = 75/263 (28%), Positives = 128/263 (48%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           +  E   Q L    ++ F E S S++S  IK+G + V+         +     L++       ++E +  ++     L+++YED +I+V+NKP GL+  P       TL N +  ++ +    N   A + HRLDK TTGL V AK  +  T+L     + +VS+ Y C+  G                +++Q M +    +  K+ ++ YRV+E+ +    + ++L TG+ HQIRVHMA I  P++GD  Y  +    F+ P
  S:    44 VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVHGGSILEL-----TAEQEAQGEWIAQDIELDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHIPDII--NVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVAQLQSRSVSRIYECIVIGVVTAGGKINAPIGRHGQQRQRMAV---MEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINFPLVGDPAYGGR----FRIP 292
>gi|92117127|ref|YP_576856.1| pseudouridine synthase, RluD [Nitrobacter hamburgensis X14] >gi|91800021|gb|ABE62396.1| ribosomal large subunit pseudouridine synthase C [Nitrobacter hamburgensis X14] (411 aa)
Score = 260, Expect = 7.4e-21, Identities = 82/265 (30%), Positives = 131/265 (49%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILN-----VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFL--NEEKQIMEIDRE-NKFNKEIITKYRVIE-QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP 268
           + +  +E N  +  F+   F  LS S I + ++ G+++VN K+     +L E D ++I  L+L   K    L+  E K I +     V++ED +++V+NKP GL  Q         L+  I   L    D       L HRLD+ T G  + AK +   T L   +   +  K Y  L  G  K K   +  ++    +EE  IM I    ++     +T Y V+E   + +A + ++ +TG+ HQ+R HMA I H ++GD KY  K N  +Q P
  S:    88 VAVTADEANMRVDRFLEARFPGLSFSHIQRVVRKGELRVNGKRADSKDRLGEGDKVRIPPLKLDTPKVAAGLSEAETK-IRDELQKMVLFEDADVMVLNKPAGLAVQGGSG-----LSRHIDGMLEVMCDAKGQRPRLVHRLDRETAGCLLVAKTRFAATALTGSFRHRSARKIYWALVAGVPKPKQGRISTYLAKEESEEDSIMRIAAHGDEGASHAVTYYAVVETSAQKLAWVSLKPVTGRTHQLRAHMAHIDHAIVGDPKYFNKEN--WQLP 354
>gi|88798806|ref|ZP_01114389.1| ribosomal large subunit pseudouridine synthase C [Reinekea sp. MED297] >gi|88778569|gb|EAR09761.1| ribosomal large subunit pseudouridine synthase C [Reinekea sp. MED297] (313 aa)
Score = 260, Expect = 7.6e-21, Identities = 76/254 (29%), Positives = 129/254 (50%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQI---FLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEA-VSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFN-KEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I +  +   Q L +F+      +  S+I + I+ G+++VN K+   + KL E D +++    +  K I+       L       +++ED  ++ VNKP GL        K+      I+    +++ + +LE  L HRLD+ T+G+ + AK +K+LT L + +  +  V K Y CL  G +      +   +  +EE    E     + N K   T +RV++Q +D A +E   +TG+ HQIRVH   +G P+LGD KY
  S:     7 IEVSADRAEQRLDNFLRYYLNNVPKSRIYRIIRKGEVRVNKKRAKPDTKLSEGDVVRVPPVTMAEKTIENPQPSAGLRKALDHAIVFEDSALLAVNKPSGLAVHGGSGLKLGL----IEALRAQRESEPFLE--LVHRLDRDTSGVVLVAKKRKSLTLLQDEFRQKTRVRKTYWCLVKGHWPDGCSVVDAPLLRHEESASGERRVSVQANGKPSRTHFRVLKQYQDCAWVEALPITGRTHQIRVHCQYVGCPILGDDKY 259
>gi|169797345|ref|YP_001715138.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii AYE] >gi|184156731|ref|YP_001845070.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii ACICU] >gi|169150272|emb|CAM88169.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii] >gi|183208325|gb|ACC55723.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii ACICU] (310 aa)
Score = 260, Expect = 7.7e-21, Identities = 77/252 (30%), Positives = 133/252 (52%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELK------LNFLEAKPILN-VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF----LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + + +  Q + +F+    K +  S+I + I+ G ++VN K+     KL   D +    R+ PI+ E K      ++   A+ +L+ V+YED+ ++VVNKP G+            +     + L     K YLE  L HR+D+ T+GL + +K + TL  L ++     + K Y  +  G+       +   +F     N E+++  + +E K +K   T++ V E+ K+  L+    L+G+ HQIRVH  SIGHP++GD KY
  S:    15 VDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQI----RVAPIRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGVAYGLI-----EALRAATGKKYLE--LIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAIVKGQVSLDKQLIDAPLFRYELANGERRV-RVSKEGKPSK---TEWVVAERFKNATLVHASPLSGRTHQIRVHGLSIGHPLVGDDKY 262
>gi|145633599|ref|ZP_01789327.1| SfhB [Haemophilus influenzae 3655] >gi|144985805|gb|EDJ92419.1| SfhB [Haemophilus influenzae 3655] (324 aa)
Score = 260, Expect = 8.1e-21, Identities = 75/255 (29%), Positives = 126/255 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHK-KTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           ++ E+  Q L   +++ F E S S++   I+   +K+N +       K+   + ++I + ++   +       EA+ I LN++YED +IIV+NKP+ L+  P       T+ N +   LY          A + HRLDK TTGL V AK     T+L        +++ Y  +  G   K     +       ++ +M +   +   K  +T YR++E  ++   L ++L TG+ HQIRVHMA I HP+LGD  Y  +
  S:    10 VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVEVEDETR------FEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNAL---LYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLMAV---HPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGR 255
>gi|148324533|gb|EDK89783.1| pseudouridylate synthase [Fusobacterium nucleatum subsp. polymorphum ATCC 10953] (316 aa)
Score = 259, Expect = 8.4e-21, Identities = 86/269 (31%), Positives = 146/269 (54%)
  Q:     9 EEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWN-YKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKK--SDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           E E   L  ++S+  +E + S + K I N  +KVN K    N  KL+  + +++      I +E  ++       L+V+YE+ + IV+NK  G++  P       TL N +  Y       N  +   + HRLDK T+GL + AKN     +L +++  + + K YLC+  G F ++  S  +++ I  + ++++ M + +EN   K  I+ YRVIEQ +  +L+E+ + TG+ HQIRVHM SI H +LGD+ Y  +     +   L +YK++F
  S:    15 EYEGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIIKKNGRKLKSGEKIEVL-----IPEEENIDIEAENIPLDVVYENDDFIVINKNYGMVVHPAYGNYTGTLVNALLYYTNNLSSVNGNIRPGIIHRLDKDTSGLILIAKNNFAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSGRIENLIGRDIKDRKKMAVVKEN--GKIAISNYRVIEQVEGYSLVEVAIETGRTHQIRVHMKSINHVILGDSVYGTEDK-NIKRQMLHAYKLEF 280
>gi|46447425|ref|YP_008790.1| putative 23S rRNA pseudouridine synthase [Candidatus Protochlamydia amoebophila UWE25] >gi|46401066|emb|CAF24515.1| putative 23S rRNA pseudouridine synthase [Candidatus Protochlamydia amoebophila UWE25] (219 aa)
Score = 259, Expect = 8.4e-21, Identities = 72/208 (34%), Positives = 110/208 (52%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL---YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNK 290
           ++++YED ++ V+NKP GL+ QP      D+L ++ K YL   Y+K    +LEA   HRLDK  +G+ V  K  K LT LN     +   K Y          +  TL++F+  N+  Q   +  ++   K     YRVIE+K   ALLEI+L TG+ HQIR  +A +G P+ GD +Y      G Q+P  T + I  + +     H +++
  S:     5 ISIVYEDNHLFVLNKPAGLLTQPSGTAH-DSLESQAKAYLKIVYQKPGNVFLEA--VHRLDKPVSGIVVFGKTSKALTRLNASVRAKQTKKIYYAWVDSVPVDEQKTLENFLIHND-FQAQVVSSKHPQAKLAKLTYRVIERKSVGALLEIKLETGRYHQIRAQLAHLGCPIRGDIRY------GSQYP-FTPHAIALHHESLEISHPIHQ 204
>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 = 259, Expect = 8.4e-21, Identities = 87/264 (32%), Positives = 140/264 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGD-------TKYNKKGN------FGFQFPCLTSYKIKFN 278
           L  ++++   ++S S I K IK+G +KVN+K     Y ++E D++ I      I +   L  L     ++++YED +++++NKP+ ++  P      +TL N I   LY  KDK       +   + HR+DK T+GL + AKN      L        +++ Y  +CYG  K+   T+   I  N + ++ M + ++ K     IT + V+E+      +  +L TG+ HQIRVH  SI HP+LGD       TK+  KG        GF  P    Y I+FN
  S:    30 LDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKARYLVKEEDNIVI-----EIPEPKVLEVLPQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGI---LYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNPKDRLKMAVVKDGK---NAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLLGDYVYGPKETKFKLKGQTLHAKKLGFIHPTTKEY-IEFN 300
>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 = 259, Expect = 8.4e-21, Identities = 76/277 (27%), Positives = 136/277 (49%)
  Q:     1 MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK---GNFGFQFPCLTSYKIKF 277
           ++Q+ ++  +E   L  +I+    +LS +     I++  + +N+++      ++  D + + L   P  + + L   EA P L ++YED +++V++KP G++  P       TL N +     E      L   + HRLD+ T+GL VAA+N + L  L        + K YL +  G+  +    +   I  +   ++ M +    +  +   T +RV+E+  + AL+E +L TG+ HQIRVH AS   PVL D  Y  K     FG     L ++++ F
  S:     6 LLQLIVEAADEGHRLDRYIAGKVPDLSRTYARHLIEDARVLLNNRQVRPASPVRVGDVVTVQL---PEPQPVGL-VAEALP-LQIVYEDDDVVVIDKPAGIVVHPAPGHNRGTLVNALIARYPEMAISGDLRPGIVHRLDRDTSGLLVAARNDRALHSLQAQQQARRMLKIYLVVVEGRMNESGGVIDAPIARHPTDRVRMAVMAGGRPAR---THWRVLEELGEYALIEARLETGRTHQIRVHFASRNRPVLADPLYGPKRPRATFGLTRQFLHAHRLGF 278
>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 = 259, Expect = 8.4e-21, Identities = 87/264 (32%), Positives = 140/264 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGD-------TKYNKKGN------FGFQFPCLTSYKIKFN 278
           L  ++++   ++S S I K IK+G +KVN+K     Y ++E D++ I      I +   L  L     ++++YED +++++NKP+ ++  P      +TL N I   LY  KDK       +   + HR+DK T+GL + AKN      L        +++ Y  +CYG  K+   T+   I  N + ++ M + ++ K     IT + V+E+      +  +L TG+ HQIRVH  SI HP+LGD       TK+  KG        GF  P    Y I+FN
  S:    18 LDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKARYLVKEEDNIVI-----EIPEPKVLEVLPQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGI---LYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNPKDRLKMAVVKDGK---NAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLLGDYVYGPKETKFKLKGQTLHAKKLGFIHPTTKEY-IEFN 288
>gi|166991830|ref|ZP_02258290.1| ribosomal large subunit pseudouridylate synthase D [Bacillus cereus AH820] (297 aa)
Score = 259, Expect = 8.7e-21, Identities = 76/255 (29%), Positives = 131/255 (51%)
  Q:     6 IKKEEENQILKDFI-SKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEA--NLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I+  EE  ++++F+ +K   + +L+ I      G I+VN +  +  ++LQ  + +++F    P+++  +    E  P L ++YED  ++V+NK   +   P +     ++ N     L    DK YL +  ++  RLD+ T+GL + AKN+     L+     +AV + Y  L +G+  ++  T+   I    +  I     E    +  IT +RVI        + ++L TG+ HQIRVHMA IGHP+LGDT Y  K
  S:    10 IESAEEGTLVREFLKTKGISKAALTDIK--FHGGAIEVNGQHASVRHQLQAGEEIRVFF---PVEERSEGMIAEDIP-LCIVYEDDAVLVINKEANMSTIPSREHPSGSVANA----LLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEALVHGEMIEQEGTIDAPIGRKSDSIIERTVCEE--GQRAITHFRVIASANHKTHVSLELDTGRTHQIRVHMAHIGHPLLGDTLYGGK 255
>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 = 259, Expect = 8.7e-21, Identities = 76/257 (29%), Positives = 121/257 (47%)
  Q:     4 IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           + +  E   Q L    S+   E S S+I   IK G ++VN K+     K+ E D +++ + L+           EA+PI L+V++ED++++V+NK    +  P       T+ N +  +     +     A + HRLDK TTGL V AK       L        + + Y C+ YG+               + +Q M + R  K   + +T YR+I + +    L ++L TG+ HQIRVHMA I H +LGD  Y  +
  S:     9 LIVPAELGEQRLDMAASELMPEYSRSRIQNWIKQGALRVNGKQVKPKEKVIEGDQVELDVELEAQGD------WEAQPIALDVVFEDEHLLVINKQADFVVHPAAGHSDGTVVNAVLHHCPALSE--LPRAGIVHRLDKDTTGLMVIAKTLIAHNSLVEQLQAREMGREYECVVYGELTGGGVVEAAIGRHPQNRQKMAVTRGGK---DAVTHYRLIRRWRGFTHLRLKLETGRTHQIRVHMAHIHHSILGDPLYGSR 255
>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 = 259, Expect = 8.7e-21, Identities = 82/266 (30%), Positives = 134/266 (50%)
  Q:     8 KEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNE-EKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------------GNFGFQFPCLTSY 273
           KE+    +   + +   + S ++I   IK G +  N K    NYK++ ND + +       K+ ++ + L     L++ YED ++ VV K +G++  P      +TL N +   +Y+ K+       +   + HR+D  T+GL + AKN      L      ++V + Y+ L +G       T+   I  N+ ++Q M +  + K   E +T + V+E  KD  L+E QL TG+ HQIRVHM  IG P++GD KY  K            G  GF+ P    Y
  S:    11 KEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLNDHIVV-----TEKEVVEADILPENLNLDIYYEDDDVAVVYKTKGMVVHPSPGHYTNTLVNGL---MYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGTIDAPIGRNKNDRQSMAVVDDGK---EAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQALHAGLIGFEHPVTGEY 282
>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 = 259, Expect = 8.8e-21, Identities = 70/238 (29%), Positives = 120/238 (50%)
  Q:    23 FKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKF----NKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           F + S S++ + I +G + VN +     Y+LQ  D + I     P++ +L+    E  P L+++YED +++VVNKP+G++  P       TL N +  +         L   + HR+DK T+GL + AK  +    L      ++  + Y+ L +G  K+   T+ D       K     DR+ +      +  +T +RV+++ +   L+  +L TG+ HQIRVHM  I HP+ GD  Y  +
  S:    26 FPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIEPE-TPVEIDLEP---ENIP-LDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYHAPLSSINGELRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKENEGTI-DAPLARSPK-----DRKKQAVVVGGRHAVTHFRVLKRYQHYTLVACRLETGRTHQIRVHMKYINHPLAGDPLYGPR 256
>gi|154492071|ref|ZP_02031697.1| hypothetical protein PARMER_01702 [Parabacteroides merdae ATCC 43184] >gi|154087857|gb|EDN86902.1| hypothetical protein PARMER_01702 [Parabacteroides merdae ATCC 43184] (359 aa)
Score = 259, Expect = 8.9e-21, Identities = 71/229 (31%), Positives = 114/229 (49%)
  Q:    29 SKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKK--DKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++I  +   G I  N K    NY+++  D + I +   P   E+     E  PI  ++YED +++VV+KP GL+  P       TL N +  YL +    D N     L HR+DK T+GL V AK  +    L+  +  +   + Y  L +G  ++    ++  I  N  ++  M +  E    K  +T Y V+E+   + L++ +L TG+ HQIRVHM  IGH +  D +Y
  S:    60 NRIQSAADAGCIMANGKPVKSNYRVKPEDVVTIMMTRPPRTFEI---LPENIPI-KIVYEDDDLLVVDKPAGLVVHPGHGNYTGTLVNALAWYLKDDPTYDPNDPALGLVHRIDKDTSGLLVVAKKPEAKAHLSMQFFHKTTKREYRALVWGIVREDEGRIEGNIGRNPRDRMQMTVFPEGDQGKTAVTHYSVLERLGYVTLVKCRLETGRTHQIRVHMKYIGHTLFNDERY 287
>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 = 259, Expect = 9.6e-21, Identities = 66/175 (37%), Positives = 99/175 (56%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYG--KFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           L V++ED++++VVNK  G++  P       TL N +   L+  KD       L   + HRLDK TTG  V AKN++ L  L   + T AV K YL L +G  K + + +TL     ++ ++   ++    K  K  +T +R  E  +  AL+E+ LLTG+ HQIRVH++  GHP+L D  Y
  S:    32 LEVLHEDRDLVVVNKAAGMVVHPGAGHASGTLVNAL---LHRVKDLAGVGGELRPGIVHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLALVHGHPKAEGRIETLYGRHPVHRQRFTGKV----KEGKSAVTVFRTREFFEGAALVEVDLLTGRTHQIRVHLSESGHPLLCDALY 205
>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 = 259, Expect = 9.8e-21, Identities = 87/264 (32%), Positives = 140/264 (53%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDK-----NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQI-MEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGD-------TKYNKKGN------FGFQFPCLTSYKIKFN 278
           L  ++++   ++S S I K IK+G +KVN+K     Y ++E D++ I      I +   L  L     ++++YED +++++NKP+ ++  P      +TL N I   LY  KDK       +   + HR+DK T+GL + AKN      L        +++ Y  +CYG  K+   T+   I  N + ++ M + ++ K     IT + V+E+      +  +L TG+ HQIRVH  SI HP+LGD       TK+  KG        GF  P    Y I+FN
  S:    30 LDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKAKYLVKEEDNIVI-----EIPEPKVLEVLPQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGI---LYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNPKDRLKMAVVKDGK---NAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLLGDFVYGPKETKFKLKGQTLHAKKLGFIHPTTKEY-IEFN 300
>gi|148653370|ref|YP_001280463.1| RluA family pseudouridine synthase [Psychrobacter sp. PRwf-1] >gi|148572454|gb|ABQ94513.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter sp. PRwf-1] (420 aa)
Score = 259, Expect = 9.8e-21, Identities = 69/255 (27%), Positives = 127/255 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYL-EANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKK--KSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           + +E+  Q +    +  F E S +++   +K+G++ VN       Y+++  D +++  +L+    +   +       L++IYED ++IV+NKP G++  P       TL N +   LY   ++ +L  A L HR+DK T+GL V  K +    EL      ++V ++Y C+  G      +  T+ D        Q  ++   +     I    ++       +LL+++L TG+ HQIRVH++ IGHP++GD  Y  +
  S:   109 VTQEQAGQRIDKLAADMFTEHSRAQLQDWLKSGNLTVNDHNEKAKYRVKIGDIVRLEAKLEQHGSDQPEDIK-----LDIIYEDDSVIVINKPVGMVVHPGAGNWSGTLVNGL---LYHYPNQAHLPRAGLVHRIDKNTSGLLVIGKTKAAQLELQEQLKDKSVYRHYQCVVAGDAPSLARQRTI-DAPIGRHRTQRTKMTVTSTGKTAITHIMKITPLSDTYSLLDVRLETGRTHQIRVHLSHIGHPIIGDDIYGNR 357
>gi|67154532|ref|ZP_00416277.1| Pseudouridine synthase, RluD [Azotobacter vinelandii AvOP] >gi|67088665|gb|EAM08131.1| Pseudouridine synthase, RluD [Azotobacter vinelandii AvOP] (317 aa)
Score = 259, Expect = 1.0e-20, Identities = 83/252 (32%), Positives = 135/252 (53%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLK------PIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKF----KKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMA-LLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           I  +   Q + +F+    K    + I + ++ G+++VN  +    YKLQ  D +++  LRL       P+ + L L  LEA     +++EDK++IV+NKP G+            +   +++   E +D   LE  L HRLD+ T+GL + AK +  L  L+     + V K YL L  G +    K+ S  L+     + E+ + E+D E +   E +T +RV+ +  D A L+E + +TG+ HQIRVH    GHP+ GD KY
  S:    16 IGPDTAGQRIDNFLRTRLKGAPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDLVRVPPLRLAERDEPVPLAQGL-LERLEAA----IVHEDKSLIVLNKPAGIAVHGGSGLSHGVIE-ALRQLRPEARD---LE--LVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYLALVRGAWPSARKQVSAPLQKNTLRSGERMV-EVDEEGR---EALTLFRVLRRFGDFATLVEAKPVTGRTHQIRVHARHAGHPIAGDAKY 264
>gi|42780396|ref|NP_977643.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus ATCC 10987] >gi|42736315|gb|AAS40251.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Bacillus cereus ATCC 10987] (297 aa)
Score = 259, Expect = 1.0e-20, Identities = 74/255 (29%), Positives = 131/255 (51%)
  Q:     6 IKKEEENQILKDFI-SKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEA--NLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           I   EE  ++++F+ +K   + +L+ I      G I+VN +  +  Y+LQ  + L++F    P+++  +    E  P L ++YED  ++V+NK   +   P +     ++ N     L    DK +L +  ++  RLD+ T+GL + AKN+     L+     +AV + Y  + +G+  ++  T+   I    +  I     E+   +  +T +RVI+       + ++L TG+ HQIRVHMA IGHP+LGD  Y  K
  S:    10 IDSAEEGTLVREFLKTKGISKAALTDIK--FHGGAIEVNGQHASVRYQLQAGEELRVFF---PVEERSEGMIAEDIP-LCIVYEDDAVLVINKEANMSTIPSREHPAGSVANA----LLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCED--GQRAVTHFRVIDSANHKTHVSLELDTGRTHQIRVHMAHIGHPLLGDNLYGGK 255
>gi|19704707|ref|NP_604269.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium nucleatum subsp. nucleatum ATCC 25586] >gi|19715021|gb|AAL95568.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium nucleatum subsp. nucleatum ATCC 25586] (319 aa)
Score = 259, Expect = 1.0e-20, Identities = 84/272 (30%), Positives = 147/272 (54%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWN-YKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKN-YLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKK--SDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           +  E E   L  ++S+  +E + S + K I N  +KVN K    N  KL+  + +++      I +E  ++       LN++YE+ + I++NK  G++  P       TL N +  Y       N  +   + HRLDK T+GL + AKN     +L +++  + + K YLC+  G F ++  S  +++ I  + ++++ M I +EN   K  I+ Y+V+EQ +  +L+E+ + TG+ HQIRVHM SI H +LGD+ Y  +     +   L +YK++F
  S:    17 VNSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIINKNGRKLKLGEKIEVL-----IPEEENIDIEPENIPLNIVYENDDFILINKSYGMVVHPAYGNYTGTLVNALLYYTNNLSSVNGNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSGRIENLIGRDSKDRKKMTIVKEN--GKIAISNYKVVEQVEGYSLVEVAIETGRTHQIRVHMKSINHVILGDSVYGTEDK-NVKRQMLHAYKLEF 285
>gi|160885528|ref|ZP_02066531.1| hypothetical protein BACOVA_03528 [Bacteroides ovatus ATCC 8483] >gi|156109150|gb|EDO10895.1| hypothetical protein BACOVA_03528 [Bacteroides ovatus ATCC 8483] (357 aa)
Score = 259, Expect = 1.0e-20, Identities = 72/231 (31%), Positives = 116/231 (50%)
  Q:    27 SLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYE--KKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLN-EEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           S ++I K+ ++G +  N K    +YK++  D + + +     + E+     E  P L ++YED  ++VVNKP GL+  P       TL N +  ++ +    D N     L HR+DK T+GL V AK     T L   +  +   + Y  L +G  ++   T+   I  N  ++  M +  +    K  +T YRV+E+   + L+E  L TG+ HQIRVHM  IGH +  D +Y
  S:    55 SRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVMMDRPRYENEI---IPENIP-LTIVYEDPYLMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRKYRALVWGVMEQDEGTIVGNIARNPRDRMQMAVMSDPTVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGHVLFNDERY 284
>gi|163939103|ref|YP_001643987.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis KBAB4] >gi|163861300|gb|ABY42359.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis KBAB4] (297 aa)
Score = 259, Expect = 1.1e-20, Identities = 74/251 (29%), Positives = 133/251 (52%)
  Q:    10 EENQILKDFI-SKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK 260
           EE  ++++F+ +K   + +L+ I    + G I+VN + T+  +KLQ  + LQIF    P+++  +   +E  P L ++YED  ++V+NK   +   P +     ++ N +  Y Y+K++      ++  RLD+ T+GL + AKN+     L+     + V + Y  + +G   ++  T+   I    +  I     E+   +  +T +RV+E   D   + ++L TG+ HQIRVHMA IGHP+LGD  Y  +
  S:    14 EEGTLVREFLKTKGISKAALTDIK--FRGGAIEVNGQHTSVRHKLQAGEELQIFF---PVEERSEGMEVEDIP-LCIVYEDDAVLVINKEANMSTIPSREHPSGSIANALL-YHYDKQNLAS-TVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVHGTILEEVGTIDAPIGRKADSIIERTVCED--GQRAVTHFRVMESSSDKTHVALELETGRTHQIRVHMAYIGHPLLGDDLYGGR 255
>gi|85713201|ref|ZP_01044230.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina baltica OS145] >gi|85692974|gb|EAQ30943.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina baltica OS145] (315 aa)
Score = 259, Expect = 1.1e-20, Identities = 76/252 (30%), Positives = 132/252 (52%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIF-LRLKPIKKELKLNFLEAKPILN--VIYEDKNIIVVNKPRGLICQPDKNEKIDTLN-NRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           + ++E  Q + +F+    + +  S + + ++ G+++VN K+T  +YK++  D+++I  +++ P K EL    L     L   ++YED   ++VNKP GL            LN   I+     +   N LE  L HRLD+ T+GL + AK +  L  L+     + ++K YL L  G+++K    ++  +  N  K    I R +   K   T++R+ ++  +  L+E   +TG+ HQIRVH    GHP+ GD KY
  S:    13 VARDEAGQRIDNFLIARLRGVPKSLVYRILRKGEVRVNKKRTKPDYKIKAGDAIRIPPVKVSP-KPELPSPKLAKVAELEQAIVYEDDAFMIVNKPSGLAVHGGSG-----LNFGLIEGLRALRPQDNALE--LVHRLDRDTSGLIMIAKKRSVLKVLHAQLRDKEMNKQYLALVRGQWQKNVRNVEAPLKKNTLKSGERIVRVDAEGKPSHTRFRINQRYAEATLVEASPVTGRTHQIRVHALHAGHPIAGDPKY 260
>gi|56460456|ref|YP_155737.1| pseudouridylate synthase Rlu family protein [Idiomarina loihiensis L2TR] >gi|56179466|gb|AAV82188.1| Predicted pseudouridylate synthase, Rlu family [Idiomarina loihiensis L2TR] (315 aa)
Score = 258, Expect = 1.1e-20, Identities = 74/272 (27%), Positives = 137/272 (50%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIK----KELKLNFLEAKPILN--VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY------NKKGNFGFQFPCLTSYKIKF 277
           +  EE  Q + +F+    + +  S + + ++ G+++ N K+   +YKL+E D     +R+ P+K     +L    LE    L   ++YED  ++++NKP G+        +   +         EK         L HR+D+ T+GL + AK +  L  L+     + ++K YL L  G+++K+  +++  +  N  K    I R +   K  +T++R+ ++ K+  L+E   +TG+ HQIRVH    GHP+  D KY      N     G     L +++++F
  S:    13 VSAEESGQRIDNFLIAQLRGVPKSLVYRIVRKGEVRANKKRIKPDYKLKEGD----LIRIPPVKVNERPDLPSANLEQVAALEHAILYEDDALMLINKPSGVAVHGGSGLQFGLIEGLRALRPKEK------SLELVHRIDRDTSGLLLVAKKRSVLRSLHEQLRNKEMNKQYLALVRGQWQKRVRSVEAPLKKNTLKSGERIVRVDAEGKASLTRFRIQQRYKEGTLVEASPVTGRTHQIRVHALHAGHPIAKDPKYGDTDFDNTMSRLGLNRLFLHAWQLRF 286
>gi|160885619|ref|ZP_02066622.1| hypothetical protein BACOVA_03622 [Bacteroides ovatus ATCC 8483] >gi|156109241|gb|EDO10986.1| hypothetical protein BACOVA_03622 [Bacteroides ovatus ATCC 8483] (223 aa)
Score = 258, Expect = 1.2e-20, Identities = 71/195 (36%), Positives = 107/195 (54%)
  Q:    83 LNVIYEDKNIIVVNKPRGLICQPDKNEKIDT-LNNRIKKYLYEKKDK-NYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEK-QIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           + V+YED +IIVVNK    I Q DK    DT L+  +K+YL EK  K   +   + HRLD+  +GL + AK  K LT LN ++ T  V K Y  +     ++    L  F+  NE++ +    D+E   +K+ I  YR+I   ++  LLE+ L TG+ HQIR  +A +G P+ GD KY    +      CL + +++F
  S:     1 MTVVYEDNHIIVVNKTASEIVQADKTG--DTPLSETVKQYLKEKYQKPGNVFLGVTHRLDRPVSGLVIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPQEPEGELVHFLVRNEKQNKSYAYDKEVPNSKKAILHYRLIGHSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGSPRSNPDGSICLHARRVRF 196
>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 = 258, Expect = 1.2e-20, Identities = 81/273 (29%), Positives = 130/273 (47%)
  Q:     5 FIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL--YEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKF 277
           F   E+ +  L  F+  S  EL+ S+I+  IK+G + VN   T   YKL+ +D + + L  K     LK   ++    LN++YED +I+V+NKP+GL+  P +     TL + +  +       + + L   + HR+DK T+GL + AK  +    L     +  + + Y+ L  G        +   I      +I          K  IT + V+   +D  LL  +L TG+ HQIRVH+A I HPV GD  Y  K         L +++++F
  S:     3 FKITEQTDSRLDHFLVAS-TELNRSQITTLIKDGLVMVNGLTTKAGYKLKNSDEITLNLEAKEETNPLKPKNID----LNIVYEDDDIMVINKPKGLVVHPSETFSETTLVSGLLHHTDTLSTHNDDPLRPGILHRIDKDTSGLILVAKTNEAHKILAQDLKSHDIKREYIALVEGVLDHNKGVIDAPI--ARHPKIRTKMAVVATGKPAITHFEVMRTFRDHTLLHCKLETGRTHQIRVHLAYIKHPVTGDPLYGTKAKILKDGQLLHAFRLEF 270
>gi|196243588|ref|ZP_03142317.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802] >gi|196208505|gb|EDY03295.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802] (318 aa)
Score = 258, Expect = 1.2e-20, Identities = 80/262 (30%), Positives = 135/262 (51%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNH-----KKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFL------NEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFG 264
           QI +  +++   +  ++S++  ++S S + K I+ G+I +N+     KKT    K+   D LQ+FL      +          P L+++YED ++I++NK  GL+  P       TL   +   LY   +           + HRLDK TTG  V AK       L      +   + YL + YG   +  DT +  I +       + K++  +  EN   +E IT ++++E+  +  L+E +L TG+ HQIRVH + IGHP++GD  Y+  G+ G
  S:    10 QIELTVQDKGDRIDLWLSQNLDQISRSHLQKLIEQGNIYLNNQVCLNKKT----KVNSGDRLQVFLPPPEPLELQPEPI----P-LDILYEDDSLIIINKSAGLVVHPAPGHTTGTL---VHGLLYHCPNLVGIGGIQRPGIVHRLDKDTTGAIVVAKTDYAHQHLQAQLKAKTARREYLGVVYG-VPRHEDTHQGTINVPIGRHRGDRKKMAVVPVENG-GREAITHWQIVERLGNYTLVEFRLETGRTHQIRVHSSYIGHPIVGDPLYSSGGSVG 272
>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 = 258, Expect = 1.3e-20, Identities = 73/266 (27%), Positives = 127/266 (47%)
  Q:    26 LSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD-----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFDKNHFLHYLNKL 291
           ++ S  +  I+ G   VN K    N KL+  D++ +      + +    + L     L+++YED +++VVNKP+G++  P       TL N +   +Y   D        +   + HR+D+ T+GL + AKN      L       + ++ Y+ +  G  K+             +++ M +  EN  ++E +T Y V +  ++  L+ ++L TG+ HQIRVHMA IGHPV GD  Y           CL + KI F      ++ + ++L
  S:    25 ITRSAAAALIEQGCCLVNGKIAAKNQKLKTGDTVTL-----DVPEAQPADILPENIPLDIVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNAL---MYHCGDSLSGINGVIRPGIVHRIDRDTSGLLIVAKNDTAHNILAEQIKVHSFTREYMAVVQGVIKEDGTVDAPIGRHKTDRKKMCVTTEN--SREAVTHYFVEQTYRNNTLVRLRLETGRTHQIRVHMAYIGHPVTGDEVYGNGSPKWLCGQCLHAKKIGFIHPDGRYMEFDSEL 285
>gi|12045231|ref|NP_073042.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37] >gi|1351560|sp|P47610|Y370_MYCGE Uncharacterized RNA pseudouridine synthase MG370 (RNA-uridine isomerase) (RNA pseudouridylate synthase) >gi|3844958|gb|AAC71597.1| pseudouridine synthase, RluA family [Mycoplasma genitalium G37] >gi|166078817|gb|ABY79435.1| pseudouridine synthase, RluA family [synthetic Mycoplasma genitalium JCVI-1.0] (323 aa)
Score = 258, Expect = 1.3e-20, Identities = 85/275 (30%), Positives = 144/275 (52%)
  Q:     3 QIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKE----LKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYL-YEKKDKNYLE--ANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIE--QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYN----KKGNFGFQFPCLTSYKIKF 277
           +  + KE ENQ +  F  K    +  S   K ++ G + +N  K   N +L+  D +     + P  +     L L+ ++ K  L +I+ED+NIIVV+KP G++CQPDK   I  L+N + K+  Y + D N L       HR+D+ T+G+ + AK  K L ELN ++    ++K Y  L +G+F         +   N    +    +     K+I T +       +KDM+L+ I+L++G+ HQIR  +    + ++GD KY+    K  N  ++   L +Y++ F
  S:     6 KFLVPKESENQRIDQFCLKILPLIKRSDFFKYLRLGKVLLNKTKPQVNTRLKTKDEIAFLFDINPYLQTNNDYLSLDLVKDK--LKIIFEDENIIVVDKPTGIVCQPDKKHSIINLSNMLLKHCGYRQFDSNKLNFYPQFAHRIDRNTSGIVIGAKTNKALKELNKVFKNNHLTKRYKGLVFGQFNHLGLQTAYWKKDNNNGIVTVKWKPFPEAKKISTFFENSSYIAQKDMSLITIRLISGRTHQIRACLNLFSNQLVGDKKYSLIQFKNRNNKYKHQALHAYELVF 291
>gi|145589104|ref|YP_001155701.1| RluA family pseudouridine synthase [Polynucleobacter sp. QLW-P1DMWA-1] >gi|145047510|gb|ABP34137.1| ribosomal large subunit pseudouridine synthase D [Polynucleobacter sp. QLW-P1DMWA-1] (318 aa)
Score = 258, Expect = 1.4e-20, Identities = 75/247 (30%), Positives = 120/247 (48%)
  Q:    15 LKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIE----QKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           L   ++ S  + S +++   ++ G + V+ K T   Y L+  +S+++F    P +   +  F      L V+YED +IIV+NKP GL+  P       TL N +     E K  +   A + HRLDK T+GL V A+     T L        V + YL   +G    +   L       +++  +++   +   K   T +R I     +   +ALLE +L TG+ HQIRVH+ S+G P++GD  Y KK 
  S:     6 LDKVLAGSLPDYSRNRLKAWVEAGAVMVDGKVTKARYLLRGGESVKVF----PQEMPEQFAFSPENIPLEVVYEDDSIIVINKPPGLVVHPAAGNWSGTLLNGLLHRFPELK--SLPRAGIVHRLDKDTSGLMVVARTAHAQTALVRQLQERTVGRRYLAWVWGDAPSQGKVLASV--GRDQRDRLKMAAGSPQGKPAATLFRRIAKGNVENAPVALLECRLETGRTHQIRVHLESLGFPLVGDPVYRKKA 248
>gi|184156035|ref|YP_001844375.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956] >gi|183227379|dbj|BAG27895.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956] (294 aa)
Score = 258, Expect = 1.4e-20, Identities = 74/228 (32%), Positives = 118/228 (51%)
  Q:    30 KISKSIKNG--DIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRE-NKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           ++   IKNG  + +V+H++     K+  N  L + ++ +P    +      ++  L ++YED N +VVNKP G+   P  +    T+ NR+K YL   KD   L  +L  RLD+ T GL + AK+    + ++       + K Y  +  G F     T   FI     +   +I+RE N   +   T+Y   E + D  L+ ++L +G+ HQIRVHMAS+GHP+LGD  Y
  S:    27 RLFNDIKNGAGEFQVDHRRVRPTTKILPNQPLTLTVQPEPGDATVA----TSEEPLTIVYEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLV-AKDAPDLRPHLITRLDRDTAGLLLVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFA----TDHGFIDAPIARIKGQIEREVNPAGQPAKTEYWAEESRGDWTLVRLRLHSGRTHQIRVHMASVGHPLLGDHLY 248
>gi|194476821|ref|YP_002049000.1| Pseudouridine synthase, RluD [Paulinella chromatophora] >gi|171191828|gb|ACB42790.1| Pseudouridine synthase, RluD [Paulinella chromatophora] (315 aa)
Score = 257, Expect = 1.5e-20, Identities = 76/256 (29%), Positives = 132/256 (51%)
  Q:    25 ELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKD----KNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF---LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFPCLTSYKIKFNFD 280
           E S S+I K I  G ++VN  K++    L++ D +QI++   P    L     +  P L++++ED+ +IVVNKP  L   P    K  TL N +   L+   D       +   + HRLDK TTG  V AK ++ L  L        VS+ Y+ + +G       T+   +    +N ++  + ++ + ++     T + +IE+  D +LL  +L TG+ HQIR+H + IG+P++GD  Y+K+      F     + ++ +F+
  S:    34 EQSRSRIQKFIYAGLVRVNGIKSSTKTPLRQGDQVQIWM---PPPDLLPYLIPQHIP-LDILFEDQYLIVVNKPADLTVHPAPGNKYGTLVNGL---LFHCSDLMGIGGEMRPGVVHRLDKSTTGCIVIAKTKEILAALQLQIQNRVVSREYIGIVHGVPATNKGTIIGKLGRHPVNRKRYAVLVNEKGRY---ACTHWCLIERWGDYSLLRFKLDTGRTHQIRIHCSHIGYPIIGDQYYSKQRRLPLAFNGQALHAVELSFN 286
>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 = 257, Expect = 1.5e-20, Identities = 73/256 (28%), Positives = 125/256 (48%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           +K  +  Q L   +++ F + S S+I + + +G I+V+ +  T    +       I L+ +   +E      EA+ I L+++YED +++V+NKPR L+  P       T+ N +    +  +      A + HRLDK TTGL V AK     T L        +++ Y  +  GK        K       ++ +M++   N+  K  +T YRV E  ++   + ++L TG+ HQIRVHM+ + HP+LGD  Y  + 
  S:    11 VKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGE-AIILQAELADEER----WEAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGTILNAL--LFHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMTAGGVVEKGISRHATKRTLMDV---NELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDIAYGGRA 257
>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 = 257, Expect = 1.5e-20, Identities = 73/256 (28%), Positives = 125/256 (48%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPI-LNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKG 261
           +K  +  Q L   +++ F + S S+I + + +G I+V+ +  T    +       I L+ +   +E      EA+ I L+++YED +++V+NKPR L+  P       T+ N +    +  +      A + HRLDK TTGL V AK     T L        +++ Y  +  GK        K       ++ +M++   N+  K  +T YRV E  ++   + ++L TG+ HQIRVHM+ + HP+LGD  Y  + 
  S:    11 VKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGE-AIILQAELADEER----WEAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGTILNAL--LFHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMTAGGVVEKGISRHATKRTLMDV---NELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLLGDIAYGGRA 257
>gi|170660217|ref|YP_001740053.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas syringae pv. tomato str. DC3000] >gi|118201620|gb|ABK79683.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas syringae pv. tomato str. DC3000] (318 aa)
Score = 257, Expect = 1.5e-20, Identities = 75/252 (29%), Positives = 129/252 (51%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIK----------KELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIF---LNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMA-LLEIQLLTGKKHQIRVHMASIGHPVLGDTKY 257
           +  E   Q + +F+    K +  + I + ++ G+++VN  +    YKLQ  D     +R+ P++           +  L  LEA     ++YEDK +IV+NKP G+                I+ +   + D   LE  L HRLD+ T+GL + AK +  L  L+     + V K Y+ L  G +      ++  +    L   ++++E++ E K   E +T ++V+ +  D A ++E + +TG+ HQIRVH    GH + GDTKY
  S:    16 VAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGD----IVRIPPVRVPERDEPVPVAQALLQRLEAA----IVYEDKALIVLNKPAGIAVHGGSGLSFGV----IEAFRQLRPDAKELE--LVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMALVRGNWATAQKQVRAPLLKSNLRSGERMVEVNEEGK---EALTLFKVLRRFGDFATMVEAKPVTGRTHQIRVHTLHAGHAIAGDTKY 264
>gi|163803777|ref|ZP_02197632.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio campbellii AND4] >gi|159172418|gb|EDP57289.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio campbellii AND4] (314 aa)
Score = 257, Expect = 1.5e-20, Identities = 75/277 (27%), Positives = 138/277 (49%)
  Q:     6 IKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILN--------VIYEDKNIIVVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEIITKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKK------GNFGFQFPCLTSYKIKFNFDKN 282
           I ++   Q + +F+    K++  S I + ++ G+++VN K+    YKL+  D     +R+ P+  E K   +     LN        +I+ED++++V+NKP G         K       I+     +    +LE  L HR+D+ T+G+ + AK +  L  L   +  + V K+Y  L  G++K     +   +  NE   I+ ++ + K ++   T+++++E+ +   L++   +TG+ HQIRVH    GHP+  D +Y  +      G  G     L +  IKF    N
  S:    13 IDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKAGD----LVRIPPVTVEQKEVDVAPSTKLNKVAELEHMIIFEDEHMLVLNKPSGTAVHGGSGLKFGA----IEALRALRPQARFLE--LVHRIDRDTSGILLVAKKRSALRYLQAQFREKTVKKFYFALVMGEWKNSCKVVNAPLLKNEVNSIVRVNPKGKPSE---TRFKILEKFEQATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFQHPSN 290