BLASTX 2.2.7 [Jan-02-2004]

Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

RID: 1075382543-32051-66168284416.BLASTQ3

Query= vorax50d06_10000_19999
         (10000 letters)


Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           1,614,176 sequences; 530,881,280 total letters

 
If you have any problems or questions with the results of this search 
please refer to the BLAST FAQs

Taxonomy reports

Related Structures

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|32472096|ref|NP_865090.1|  tRNA pseudouridine synthase A ...   159   3e-37 
gi|25010174|ref|NP_734569.1|  Unknown [Streptococcus agalact...   155   3e-36 
gi|22536285|ref|NP_687136.1|  tRNA pseudouridine synthase A ...   154   6e-36 
gi|18309973|ref|NP_561907.1|  tRNA-pseudouridine synthase I ...   153   1e-35 
gi|23022300|ref|ZP_00061912.1|  COG0101: Pseudouridylate syn...   152   3e-35 
gi|18311353|ref|NP_563287.1|  tRNA-pseudouridine synthase I ...   150   1e-34 
gi|22991322|ref|ZP_00036055.1|  COG0101: Pseudouridylate syn...   147   6e-34 
gi|24378608|ref|NP_720563.1|  putative tRNA pseudouridine sy...   144   7e-33 
gi|30018411|ref|NP_830042.1|  tRNA pseudouridine synthase A ...   141   6e-32 
gi|23054523|ref|ZP_00080680.1|  COG0101: Pseudouridylate syn...   141   6e-32 
gi|3915176|sp|Q45557|TRUA_BACSP  tRNA pseudouridine synthase...   140   7e-32 
gi|21398100|ref|NP_654085.1|  PseudoU_synth_1, tRNA pseudour...   140   1e-31 
gi|15675714|ref|NP_269888.1|  putative tRNA pseudouridine sy...   139   2e-31 
gi|15901439|ref|NP_346043.1|  tRNA pseudouridine synthase A ...   139   2e-31 
gi|20808627|ref|NP_623798.1|  Pseudouridylate synthase (tRNA...   139   2e-31 
gi|16801808|ref|NP_472076.1|  highly similar to pseudouridyl...   139   3e-31 
gi|21911175|ref|NP_665443.1|  putative tRNA pseudouridine sy...   138   4e-31 
gi|15903494|ref|NP_359044.1|  tRNA pseudouridine synthase A ...   137   8e-31 
gi|15896350|ref|NP_349699.1|  Pseudouridylate synthase, TRUA...   137   8e-31 
gi|16804636|ref|NP_466121.1|  highly similar to pseudouridyl...   135   2e-30 
gi|28211488|ref|NP_782432.1|  tRNA pseudouridine synthase A ...   134   5e-30 
gi|22993077|ref|ZP_00037688.1|  COG0101: Pseudouridylate syn...   134   7e-30 
gi|15612730|ref|NP_241033.1|  tRNA pseudouridine synthase A ...   133   1e-29 
gi|30018678|ref|NP_830309.1|  tRNA pseudouridine synthase A ...   133   2e-29 
gi|28212149|ref|NP_783093.1|  tRNA pseudouridine synthase A ...   131   4e-29 
gi|13358100|ref|NP_078374.1|  pseudouridylate synthase I [Ur...   131   6e-29 
gi|23024296|ref|ZP_00063512.1|  COG0101: Pseudouridylate syn...   130   8e-29 
gi|16077216|ref|NP_388029.1|  pseudouridylate synthase I [Ba...   129   2e-28 
gi|23003456|ref|ZP_00047118.1|  COG0101: Pseudouridylate syn...   129   2e-28 
gi|23097605|ref|NP_691071.1|  tRNA pseudouridine synthase A ...   129   2e-28 
gi|37527059|ref|NP_930403.1|  tRNA pseudouridine synthase A ...   126   1e-27 
gi|15672468|ref|NP_266642.1|  tRNA pseudouridine synthase A ...   126   1e-27 
gi|39997968|ref|NP_953919.1|  tRNA pseudouridine synthase A ...   126   2e-27 
gi|33519947|ref|NP_878779.1|  tRNA pseudouridine synthase A ...   126   2e-27 
gi|15677859|ref|NP_275027.1|  tRNA pseudouridine synthase A ...   125   3e-27 
gi|13431951|sp|Q9PJT0|TRUA_CHLMU  tRNA pseudouridine synthas...   125   3e-27 
gi|15793409|ref|NP_283231.1|  tRNA pseudouridine synthase [N...   124   5e-27 
gi|23473971|ref|ZP_00129266.1|  COG0101: Pseudouridylate syn...   124   9e-27 
gi|27468710|ref|NP_765347.1|  tRNA pseudouridine synthase A ...   123   1e-26 
gi|15598310|ref|NP_251804.1|  tRNA-pseudouridine synthase I ...   123   2e-26 
gi|23062372|ref|ZP_00087161.1|  COG0101: Pseudouridylate syn...   122   3e-26 
gi|27262396|gb|AAN87479.1|  tRNA pseudouridine synthase A [H...   122   4e-26 
gi|40062661|gb|AAR37582.1|  tRNA pseudouridine synthase A [u...   121   5e-26 
gi|15605190|ref|NP_219976.1|  Pseudouridylate Synthase I [Ch...   121   6e-26 
gi|30248700|ref|NP_840770.1|  tRNA pseudouridine synthase [N...   120   1e-25 
gi|22125494|ref|NP_668917.1|  pseudouridylate synthase I [Ye...   120   1e-25 
gi|16122970|ref|NP_406283.1|  tRNA pseudouridine synthase A ...   120   1e-25 
gi|22965972|ref|ZP_00013570.1|  COG0101: Pseudouridylate syn...   119   2e-25 
gi|39938715|ref|NP_950481.1|  pseudouridylate synthase [Onio...   117   7e-25 
gi|33596565|ref|NP_884208.1|  tRNA pseudouridine synthase A ...   117   7e-25 
gi|17546704|ref|NP_520106.1|  PROBABLE TRNA PSEUDOURIDINE SY...   117   9e-25 
gi|15616818|ref|NP_240030.1|  pseudouridylate synthase I [Bu...   117   1e-24 
gi|17988610|ref|NP_541243.1|  TRNA PSEUDOURIDINE SYNTHASE A ...   117   1e-24 
gi|19704921|ref|NP_602416.1|  tRNA pseudouridine synthase A ...   116   1e-24 
gi|33592579|ref|NP_880223.1|  tRNA pseudouridine synthase A ...   116   2e-24 
gi|23472932|ref|ZP_00128252.1|  COG0101: Pseudouridylate syn...   115   3e-24 
gi|22977202|ref|ZP_00023021.1|  COG0101: Pseudouridylate syn...   115   3e-24 
gi|23467218|ref|ZP_00122802.1|  COG0101: Pseudouridylate syn...   115   3e-24 
gi|32030346|ref|ZP_00133213.1|  COG0101: Pseudouridylate syn...   115   3e-24 
gi|15644322|ref|NP_229374.1|  pseudouridylate synthase I [Th...   115   3e-24 
gi|30913405|sp|Q93NE2|TRUA_MYXXA  tRNA pseudouridine synthas...   115   4e-24 
gi|22957777|ref|ZP_00005466.1|  COG0101: Pseudouridylate syn...   115   4e-24 
gi|34762680|ref|ZP_00143671.1|  tRNA pseudouridine synthase ...   114   6e-24 
gi|15836112|ref|NP_300636.1|  pseudouridylate synthase I [Ch...   114   6e-24 
gi|15925209|ref|NP_372743.1|  tRNA pseudouridine synthase A ...   114   6e-24 
gi|16124533|ref|NP_419097.1|  tRNA pseudouridine synthase [C...   114   6e-24 
gi|15618490|ref|NP_224776.1|  Pseudouridylate Synthase I [Ch...   114   6e-24 
gi|16273533|ref|NP_439786.1|  pseudouridylate synthase I [Ha...   114   7e-24 
gi|22986697|ref|ZP_00031789.1|  COG0101: Pseudouridylate syn...   114   7e-24 
gi|8569326|pdb|1DJ0|A  Chain A, The Crystal Structure Of E. ...   113   1e-23 
gi|15887719|ref|NP_353400.1|  AGR_C_644p [Agrobacterium tume...   113   1e-23 
gi|16130253|ref|NP_416821.1|  pseudouridylate synthase I [Es...   113   1e-23 
gi|15594358|ref|NP_212146.1|  pseudouridylate synthase I (hi...   113   2e-23 
gi|24113690|ref|NP_708200.1|  pseudouridylate synthase I [Sh...   112   2e-23 
gi|16761293|ref|NP_456910.1|  tRNA pseudouridine synthase A ...   112   2e-23 
gi|15802865|ref|NP_288892.1|  pseudouridylate synthase I [Es...   112   2e-23 
gi|16765695|ref|NP_461310.1|  pseudouridylate synthase I [Sa...   112   2e-23 
gi|28971662|dbj|BAC65262.1|  tRNA pseudouridine synthase [Bu...   112   3e-23 
gi|23103825|ref|ZP_00090299.1|  COG0101: Pseudouridylate syn...   112   3e-23 
gi|1665842|emb|CAA70351.1|  pseudouridylate synthase I [Borr...   112   3e-23 
gi|31544780|ref|NP_853358.1|  TruA [Mycoplasma gallisepticum...   112   4e-23 
gi|33152228|ref|NP_873581.1|  tRNA pseudouridine synthase A;...   111   5e-23 
gi|23038086|ref|ZP_00070270.1|  COG0101: Pseudouridylate syn...   111   5e-23 
gi|21283867|ref|NP_646955.1|  tRNA pseudouridine synthase A ...   111   5e-23 
gi|34498219|ref|NP_902434.1|  pseudouridylate synthase  A [C...   111   5e-23 
gi|22962614|ref|ZP_00010220.1|  COG0101: Pseudouridylate syn...   111   6e-23 
gi|15641014|ref|NP_230645.1|  tRNA pseudouridine synthase A ...   110   8e-23 
gi|23121165|ref|ZP_00103551.1|  COG0101: Pseudouridylate syn...   109   2e-22 
gi|27383218|ref|NP_774747.1|  tRNA pseudouridine synthase I ...   109   2e-22 
gi|21672480|ref|NP_660547.1|  tRNA pseudouridine synthase A ...   109   2e-22 
gi|29349645|ref|NP_813148.1|  tRNA pseudouridine synthase A ...   109   2e-22 
gi|15602502|ref|NP_245574.1|  TruA [Pasteurella multocida] >...   109   2e-22 
gi|28898964|ref|NP_798569.1|  tRNA pseudouridine synthase A ...   108   3e-22 
gi|27365335|ref|NP_760863.1|  tRNA pseudouridine synthase A ...   108   4e-22 
gi|28377870|ref|NP_784762.1|  pseudouridylate synthase A [La...   108   5e-22 
gi|15964174|ref|NP_384527.1|  PROBABLE TRNA PSEUDOURIDINE SY...   107   7e-22 
gi|27904686|ref|NP_777812.1|  tRNA pseudouridine synthase A ...   107   1e-21 
gi|22999743|ref|ZP_00043708.1|  COG0101: Pseudouridylate syn...   105   3e-21 
gi|15807281|ref|NP_296011.1|  pseudouridylate synthase I [De...   103   1e-20 
gi|24212681|sp|Q9ZCA3|TRUA_RICPR  tRNA pseudouridine synthas...   103   1e-20 

Alignments


>gi|32472096|ref|NP_865090.1|   tRNA pseudouridine synthase A [Pirellula sp. 1]
 gi|32397468|emb|CAD72774.1|   tRNA pseudouridine synthase A [Pirellula sp.]
          Length = 276

 Score =  159 bits (401), Expect = 3e-37
 Identities = 93/255 (36%), Positives = 142/255 (55%), Gaps = 2/255 (0%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            + + + Y GT+Y GWQ QP   ++IQ +LE+ ++ ++    +  +GSGRTD+GVHA+GQV
Sbjct: 10   FHLTVAYDGTEYCGWQVQPE-QRSIQSELERVIRPLA-GRPVRVLGSGRTDAGVHAIGQV 67

Query: 3032 VRVQIPL-ELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRR 3208
             R  +P+ + + ++L +A+NS LPNDI       + E F+P+ DA  K Y+YL  + G R
Sbjct: 68   ARCVLPVWKADTVALQRAINSKLPNDIRVKAVRETRERFHPIADATGKQYQYLVQVGGSR 127

Query: 3209 NALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQ 3388
            +   +  +  +  P+D   M+ A   F+G HDF  F   G +  STVR I+  +      
Sbjct: 128  DPFANRFVNRVGGPIDHSAMQSAAAKFVGRHDFKAFQGTGAERPSTVRTIHSARWIPRVA 187

Query: 3389 QGFLG-EVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLA 3565
             G  G E+  EH+ FE+ G GFL  MVR ++GT+  +G GK     +   L S       
Sbjct: 188  TGPTGAELEGEHWCFEIDGEGFLYNMVRNLMGTMLEVGRGKKSPNWIDEVLASRDRKMAG 247

Query: 3566 AVAPSNGLYLCEVNY 3610
              AP  GL+LC V+Y
Sbjct: 248  PTAPPQGLFLCRVDY 262



>gi|25010174|ref|NP_734569.1|   Unknown [Streptococcus agalactiae NEM316]
 gi|23094525|emb|CAD45744.1|   Unknown [Streptococcus agalactiae NEM316]
          Length = 258

 Score =  155 bits (392), Expect = 3e-36
 Identities = 87/253 (34%), Positives = 143/253 (56%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK  + Y G+ + G+Q+QP+  +T+Q ++E+ LK+++  +++   G+GRTD+GVHA GQV
Sbjct: 4    YKAQISYDGSAFSGFQRQPNC-RTVQEEIERTLKRLNSGNDVIIHGAGRTDAGVHAYGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +   +P   +   L   L++  P+DI+ +  E  S+ F+  +D   KTY++L  +   +N
Sbjct: 63   IHFDLPQARDVEKLRFGLDTQCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIGRPKN 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             ++ +  T    P+ IE M+EA +  +G HDF  F   GT + + VR I+D K+  E  +
Sbjct: 123  PMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQFEASK 182

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
              L        IF   G+GFL + VR MVGTL  IG G++ ++ +K  L + +       
Sbjct: 183  NLL--------IFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPT 234

Query: 3572 APSNGLYLCEVNY 3610
            A  NGLYL E+ Y
Sbjct: 235  AAGNGLYLKEIIY 247



>gi|22536285|ref|NP_687136.1|   tRNA pseudouridine synthase A [Streptococcus agalactiae 2603V/R]
 gi|22533107|gb|AAM99008.1|   tRNA pseudouridine synthase A [Streptococcus agalactiae 2603V/R]
          Length = 258

 Score =  154 bits (389), Expect = 6e-36
 Identities = 87/253 (34%), Positives = 142/253 (56%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK  + Y G+ + G+Q+QP+  +T+Q ++E+ LK+++  +++   G+GRTD GVHA GQV
Sbjct: 4    YKAQISYDGSAFSGFQRQPNC-RTVQEEIERTLKRLNSGNDVIIHGAGRTDVGVHAYGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +   +P   +   L   L++  P+DI+ +  E  S+ F+  +D   KTY++L  +   +N
Sbjct: 63   IHFDLPQARDVEKLRFGLDTQCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIGRPKN 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             ++ +  T    P+ IE M+EA +  +G HDF  F   GT + + VR I+D K+  E  +
Sbjct: 123  PMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQFEASK 182

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
              L        IF   G+GFL + VR MVGTL  IG G++ ++ +K  L + +       
Sbjct: 183  NLL--------IFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPT 234

Query: 3572 APSNGLYLCEVNY 3610
            A  NGLYL E+ Y
Sbjct: 235  AAGNGLYLKEIIY 247



>gi|18309973|ref|NP_561907.1|   tRNA-pseudouridine synthase I [Clostridium perfringens]
 gi|24212547|sp|Q8XLQ0|TRUA_CLOPE   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|18144651|dbj|BAB80697.1|   tRNA-pseudouridine synthase I [Clostridium perfringens str. 13]
          Length = 248

 Score =  153 bits (387), Expect = 1e-35
 Identities = 91/255 (35%), Positives = 138/255 (54%), Gaps = 3/255 (1%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQ---TIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALG 3025
            KI L Y G++Y+GWQKQ        T+Q +LEK L K++ S+EI  IG GRTDSGVHA  
Sbjct: 5    KITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVLTKMT-SEEIQLIGCGRTDSGVHAKN 63

Query: 3026 QVVRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGR 3205
             V   +    +    +++ +N +LP DI       +SE F+  F+ K KTY+Y    N  
Sbjct: 64   YVANFKTNSLMTLEQIIEYINEYLPEDIRVTEIREASERFHARFNVKSKTYEYTIDNNKF 123

Query: 3206 RNALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEK 3385
            ++  +      ++  +D+E M E  +  +G HDF  F ++ +   ST+R I   + H  +
Sbjct: 124  KDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKSTLRTINSIEFH--E 181

Query: 3386 QQGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLA 3565
                L          ++ G+GFL  MVR+MVGTL ++GLGK+E   +   L +   AK +
Sbjct: 182  NNNILS--------IKINGNGFLLNMVRIMVGTLVDVGLGKIEPKYINDILEAKERAKAS 233

Query: 3566 AVAPSNGLYLCEVNY 3610
              AP++GL L E+NY
Sbjct: 234  EKAPAHGLCLLELNY 248



>gi|23022300|ref|ZP_00061912.1|   COG0101: Pseudouridylate synthase [Clostridium thermocellum ATCC
            27405]
          Length = 281

 Score =  152 bits (383), Expect = 3e-35
 Identities = 89/252 (35%), Positives = 134/252 (53%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K+I+ Y GT Y GWQKQ + ++T+Q  +E+A+K ++  +++  IG+ RTD GVHALGQV 
Sbjct: 42   KLIIEYDGTNYHGWQKQKN-AKTVQDTIERAIKGLT-GEKVDLIGASRTDFGVHALGQVA 99

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
                   +       ALN  LP+DI    S+     F+  + AK K Y+YL   +   +A
Sbjct: 100  NFITNSGIPGDRFSYALNRMLPDDIVIKESQEVDMDFHARYKAKGKRYRYLIYNSQFPSA 159

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQG 3394
            L+      +   +D E M+ A   F+G HDF+ F + G+   ++VR I D  L  E +  
Sbjct: 160  LLRHRTYHVSHKLDFESMQRAASYFLGTHDFSAFRSSGSSAKTSVRTITDVSLEREDKI- 218

Query: 3395 FLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVA 3574
                       FE+ G GFL  MVR++VGTL  +G+GK+   ++   + S    +    A
Sbjct: 219  ---------VKFEIAGDGFLYNMVRIIVGTLMEVGIGKIRADEIPQIIESRKRKRAGRTA 269

Query: 3575 PSNGLYLCEVNY 3610
            P+ GLYL EV Y
Sbjct: 270  PAEGLYLVEVYY 281



>gi|18311353|ref|NP_563287.1|   tRNA-pseudouridine synthase I [Clostridium perfringens]
 gi|18146037|dbj|BAB82077.1|   tRNA-pseudouridine synthase I [Clostridium perfringens str. 13]
          Length = 244

 Score =  150 bits (378), Expect = 1e-34
 Identities = 95/252 (37%), Positives = 138/252 (54%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K+ + Y GT Y GWQKQP    TIQ ++E+A+KK++K +E+  +GS RTDSGVHA   V 
Sbjct: 5    KLTIEYDGTSYFGWQKQP-IGNTIQQKVEEAIKKVTK-EEVEILGSSRTDSGVHAKAYVA 62

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
              +    +   +   ALNS LP DI  I+SE  +E F+  +    KTY Y         A
Sbjct: 63   NFKTNSNIPGKNFKAALNSKLPKDIVIINSEEVAEDFHARYMTTGKTYCYTILNREEPPA 122

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQG 3394
            L  + +  + + +D+E M+EAC+ F+G+HDF  F   G  + ++VR I D  +H+E  +G
Sbjct: 123  LERNYVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITD--IHIE-TEG 179

Query: 3395 FLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVA 3574
               ++Y       V   GFL  MVRL+VGTL  +G GK +   +K  ++S    K     
Sbjct: 180  NKIKIY-------VSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKAGICV 232

Query: 3575 PSNGLYLCEVNY 3610
            P  GL L +V Y
Sbjct: 233  PPTGLCLEKVFY 244



>gi|22991322|ref|ZP_00036055.1|   COG0101: Pseudouridylate synthase [Enterococcus faecium]
          Length = 248

 Score =  147 bits (372), Expect = 6e-34
 Identities = 86/253 (33%), Positives = 135/253 (53%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK I+ Y GT + G+QKQP+  +T+Q ++EK L+K++   EI   GSGRTD+GVHA+GQV
Sbjct: 4    YKAIIAYDGTNFNGFQKQPN-GRTVQEEVEKTLQKMANGKEITVFGSGRTDAGVHAIGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +    P E     +  AL++  P DI     E  SE F+  +  K+KTY++   +   R+
Sbjct: 63   IHFDYPEERPLERMRFALDTQSPEDIAVRQVEIVSEDFHARYLVKEKTYQFRVDIGKPRS 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
                   +    P+D+EK++ A    +G HDF  F   G+ I   +R IY+ K+ + + +
Sbjct: 123  PFRRHYASYFPYPLDLEKIQRALPDLLGTHDFTSFCASGSSIEDKIRTIYEAKMEVNETK 182

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
                    +  +F  +G+GFL +M+R++VGTL  IG G++    +   +           
Sbjct: 183  --------DELLFTFRGNGFLYKMIRILVGTLLKIGNGRLPEDSIPDIIAKKDRNAAGPT 234

Query: 3572 APSNGLYLCEVNY 3610
            A   GLYL EV Y
Sbjct: 235  AHPEGLYLYEVKY 247



>gi|24378608|ref|NP_720563.1|   putative tRNA pseudouridine synthase A [Streptococcus mutans UA159]
 gi|38258780|sp|Q8DWH1|TRUA_STRMU   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|24376463|gb|AAN57869.1|   putative tRNA pseudouridine synthase A [Streptococcus mutans UA159]
          Length = 249

 Score =  144 bits (363), Expect = 7e-33
 Identities = 87/253 (34%), Positives = 133/253 (52%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK I+ Y GT + G+Q+QP   +T+Q ++EK L +++    +   G+GRTD+GVHA GQV
Sbjct: 4    YKAIISYDGTNFSGFQRQPQV-RTVQEEIEKTLLRLNSGQAVKIHGAGRTDAGVHAYGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +   +P + +   L   L++  P+DI+ I  E  ++ F+  +    KTY++L  L   +N
Sbjct: 63   IHFDLPQQRDLEKLRFGLDTQTPDDIDVIQVEQVADDFHARYQKHRKTYEFLVDLGRPKN 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             L+    T     +D   ++ A +   G HDF  F   GT + + VR I    +  + + 
Sbjct: 123  PLMRHYATHFPYKVDFSVVKAAIKKLRGTHDFTGFTASGTSVENKVRTISRATVEKDDKT 182

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
            GFL        IF   GSGFL + VR MVGTL  IG G++ +  +   L S   +     
Sbjct: 183  GFL--------IFTFTGSGFLYKQVRNMVGTLLKIGNGRMPIDQIDRILESGDRSLAGPT 234

Query: 3572 APSNGLYLCEVNY 3610
            A SNGLYL E+ Y
Sbjct: 235  AASNGLYLKEIIY 247



>gi|30018411|ref|NP_830042.1|   tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|29893951|gb|AAP07243.1|   tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
          Length = 252

 Score =  141 bits (355), Expect = 6e-32
 Identities = 91/252 (36%), Positives = 136/252 (53%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K  + Y G  + G+Q QP+  +T+Q ++EKAL+K+ K + +    SGRTDS VHA GQV+
Sbjct: 10   KCTVAYDGMHFCGYQIQPN-HRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKGQVI 68

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
                PL LE      ALN+ LP+DI     E  +E F+  +  + K Y+Y   L+   + 
Sbjct: 69   HFDTPLSLEEWQWSNALNTMLPDDIVIRQVEKKTEEFHARYGVEKKEYRYRVLLSKTADV 128

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQG 3394
               + +     P++I  +R+A   FIG HDF  F +  TD    VR IY+ +L +E+   
Sbjct: 129  FRRNYVYQYPYPLEINSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIEL-IEQD-- 185

Query: 3395 FLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVA 3574
                   +  IF   G+GFL  MVR++VGTL ++G GK++   +   L   +      +A
Sbjct: 186  -------DEIIFRFVGNGFLYNMVRIIVGTLLSVGQGKLDPDSIPEILAKQNRQFAGKMA 238

Query: 3575 PSNGLYLCEVNY 3610
            P +GLYL EVNY
Sbjct: 239  PGHGLYLWEVNY 250



>gi|23054523|ref|ZP_00080680.1|   COG0101: Pseudouridylate synthase [Geobacter metallireducens]
          Length = 256

 Score =  141 bits (355), Expect = 6e-32
 Identities = 92/252 (36%), Positives = 127/252 (50%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K++L Y GT Y GWQ QP+   ++Q  +E+AL ++ K + +    SGRTD+GVHA G V 
Sbjct: 17   KLVLEYDGTNYAGWQIQPN-GISVQQVVEEALARLLK-EPVRVHSSGRTDAGVHARGMVA 74

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
                   L   +    LN+ LP DI  + +  + + FNP FDA  K Y+Y      RR+ 
Sbjct: 75   AFTTAKGLPMRAFSDGLNALLPPDIAVMEALEAPDGFNPRFDAAGKHYRYTIHRGERRSP 134

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQG 3394
            L    +      +D+  M +     +GEHDFA F T G    +TVR I    L LE    
Sbjct: 135  LCRHYVWHARETLDLAAMEKGASHMVGEHDFASFRTAGCAARTTVRRIDAVDLALE---- 190

Query: 3395 FLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVA 3574
              G++       +VKGSGFL+ MVR+MVGTL  +G G+    D+ +    P        A
Sbjct: 191  --GDLLH----IDVKGSGFLRNMVRIMVGTLVEVGRGRRSADDVALLFRYPGERFAGPTA 244

Query: 3575 PSNGLYLCEVNY 3610
            P  GL L EV Y
Sbjct: 245  PPQGLCLMEVYY 256



>gi|3915176|sp|Q45557|TRUA_BACSP   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|80158|pir||JT0612   tRNA-pseudouridine synthase I (EC 5.4.99.12) - Bacillus sp.  (strain
            KSM-64)
 gi|289265|gb|AAA73188.1|   unknown [Bacillus sp. KSM-64]
          Length = 244

 Score =  140 bits (354), Expect = 7e-32
 Identities = 86/253 (33%), Positives = 136/253 (53%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK++++Y G +Y+GWQ+  +   TIQG++E  L ++    +I  IGSGRTD+GVHALGQV
Sbjct: 4    YKLMIQYDGGRYKGWQRLGNGENTIQGKIETVLSEMV-GRKIEIIGSGRTDAGVHALGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
              V++        + + LN +LP+DI         + F+  ++AKDKTY Y        +
Sbjct: 63   ANVKLSENFTVKEVKEYLNRYLPHDISVTEVTLVPDRFHSRYNAKDKTYLYKIWNEDYTH 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
              +      +++ + I+ M +A +LF+GEHDF  F    +   +  R I+   + ++  Q
Sbjct: 123  PFMRKYSLHIEKKLHIDNMVKASQLFVGEHDFTAFSNAKSKKKTNTRTIH--SITIQDNQ 180

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
            GF+           V G GFL  MVR MVGTL  +GLG+ E   +   L S   ++ A  
Sbjct: 181  GFID--------IRVCGDGFLYNMVRKMVGTLIEVGLGEKEPEQVLTILESKDRSQ-AGF 231

Query: 3572 APSNGLYLCEVNY 3610
            A + GLYL  +++
Sbjct: 232  ADATGLYLEGISF 244



>gi|21398100|ref|NP_654085.1|   PseudoU_synth_1, tRNA pseudouridine synthase [Bacillus anthracis
            A2012]
          Length = 252

 Score =  140 bits (353), Expect = 1e-31
 Identities = 89/252 (35%), Positives = 135/252 (53%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K  + Y G  + G+Q QP   +T+Q ++EKAL+K+ K + +    SGRTDS VHA GQV+
Sbjct: 10   KCTVAYDGMHFCGYQIQPQ-HRTVQQEIEKALQKLHKGELVRVQASGRTDSTVHAKGQVI 68

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
                PL LE      ALN+ LP+DI     E  +E F+  +  + K Y+Y   ++   + 
Sbjct: 69   HFDTPLSLEEWQWSNALNTMLPDDIVITQVEKKTEEFHARYGVERKEYRYRVLVSKTADV 128

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQG 3394
               + +     P+++  +R+A   FIG HDF  F +  TD    VR IY+ +L +E+   
Sbjct: 129  FRRNYVYQYPYPLEVNSIRKAIPYFIGTHDFTSFCSAKTDKKDKVRTIYEIEL-IEQD-- 185

Query: 3395 FLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVA 3574
                   +  IF   G+GFL  MVR++VGTL N+G GK++   +   L   +      +A
Sbjct: 186  -------DELIFRFVGNGFLYNMVRIIVGTLLNVGQGKLDPDSIPEILAKQNRQFAGKMA 238

Query: 3575 PSNGLYLCEVNY 3610
            P +GLYL +VNY
Sbjct: 239  PGHGLYLWQVNY 250



>gi|15675714|ref|NP_269888.1|   putative tRNA pseudouridine synthase A (pseudouridylate synthase I)
            [Streptococcus pyogenes]
 gi|19746822|ref|NP_607958.1|   putative tRNA pseudouridine synthase A [Streptococcus pyogenes
            MGAS8232]
 gi|25009504|sp|Q99Y28|TRUA_STRPY   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|13622931|gb|AAK34609.1|   putative tRNA pseudouridine synthase A (pseudouridylate synthase I)
            [Streptococcus pyogenes M1 GAS]
 gi|19749059|gb|AAL98457.1|   putative tRNA pseudouridine synthase A [Streptococcus pyogenes
            MGAS8232]
          Length = 249

 Score =  139 bits (351), Expect = 2e-31
 Identities = 86/253 (33%), Positives = 137/253 (54%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK  + Y GT + G+Q+Q H  +T+Q ++EK L K++   +I   G+GRTD+GVHA GQV
Sbjct: 4    YKATISYDGTLFSGFQRQRHL-RTVQEEIEKTLYKLNNGTKIIIHGAGRTDAGVHAYGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +   +P E E   L  AL++  P DI+ ++ E  ++ F+  +    KTY++L      +N
Sbjct: 63   IHFDLPQEQEVEKLRFALDTQTPEDIDVVNIEKVADDFHCRYQKHLKTYEFLVDNGRPKN 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             ++    T     ++I+ M+EA    +G HDF  F   GT + + VR I    +  +++ 
Sbjct: 123  PMMRHYTTHYPYTLNIKLMQEAINGLVGTHDFTGFTAAGTSVQNKVRTITKATVSRDEKT 182

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
             FL        +F   G+GFL + VR MVGTL  IG G++ +  +K+ L+S +       
Sbjct: 183  DFL--------VFTFSGNGFLYKQVRNMVGTLLKIGNGQMPVEQVKVILSSKNRQLAGPT 234

Query: 3572 APSNGLYLCEVNY 3610
               NGLYL E+ Y
Sbjct: 235  ISGNGLYLKEICY 247



>gi|15901439|ref|NP_346043.1|   tRNA pseudouridine synthase A [Streptococcus pneumoniae TIGR4]
 gi|25453312|sp|Q97PL0|TRUA_STRPN   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|25292035|pir||B95186   tRNA pseudouridine synthase A [imported] - Streptococcus pneumoniae
            (strain TIGR4)
 gi|14973090|gb|AAK75683.1|   tRNA pseudouridine synthase A [Streptococcus pneumoniae TIGR4]
          Length = 249

 Score =  139 bits (350), Expect = 2e-31
 Identities = 84/253 (33%), Positives = 133/253 (52%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK  + Y G  + G+Q+QPH ++++Q ++EK L +++K   I   G+GRTDSGVHALGQV
Sbjct: 4    YKATISYDGYAFAGFQRQPH-ARSVQEEIEKTLTRLNKGQAITVHGAGRTDSGVHALGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +   +P +++   L  AL++  P DI+ I  E  ++ F+  +    KTY++       +N
Sbjct: 63   IHFDLPYQMDEEKLRFALDTQSPEDIDVISIELVADDFHCRYAKHSKTYEFTVDRGRPKN 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             +     T    P+D+E+M+ A +   G HDF  F   GT +   VR I +  L +++  
Sbjct: 123  PMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIVDETG 182

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
             FL         F   G+GFL + +R MVGTL  IG  ++ +  + + L           
Sbjct: 183  QFL--------TFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPT 234

Query: 3572 APSNGLYLCEVNY 3610
            A  NGLYL E+ Y
Sbjct: 235  AAPNGLYLKEIRY 247



>gi|20808627|ref|NP_623798.1|   Pseudouridylate synthase (tRNA psi55) [Thermoanaerobacter
            tengcongensis]
 gi|24212532|sp|Q8R7Y7|TRUA_THETN   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|20517260|gb|AAM25402.1|   Pseudouridylate synthase (tRNA psi55) [Thermoanaerobacter
            tengcongensis]
          Length = 240

 Score =  139 bits (350), Expect = 2e-31
 Identities = 86/251 (34%), Positives = 137/251 (54%)
 Frame = +2

Query: 2858 IILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVVR 3037
            +I+ Y GT Y GWQ Q +   T+Q  LEKA++K++  ++++ IGS RTD+GVHAL QV  
Sbjct: 2    LIIEYDGTNYHGWQYQKNAI-TVQEVLEKAIEKVT-GEKVNLIGSSRTDTGVHALYQVAN 59

Query: 3038 VQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNAL 3217
             +   ++ P  L  ALN+ LP+D+  + ++   + F+  + A+ K Y+YL          
Sbjct: 60   FKTKTKIPPEKLPYALNAVLPDDVVVVKAKEVDKSFHARYSARSKRYRYLILNRQFPMPT 119

Query: 3218 VDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGF 3397
            + +    +  P+D+E M++A   F G HDF+ F   G    + V+ I+D  L +EK+   
Sbjct: 120  MRNYCWHVPYPLDVEAMKKAAFFFRGTHDFSAFKASGNKKVNPVKTIFD--LTVEKEGDL 177

Query: 3398 LGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAP 3577
            +          EV+  GFL  MVR++VGTL  +GLGK++  ++   + S    K    AP
Sbjct: 178  IK--------IEVEADGFLYNMVRIIVGTLVYVGLGKIKAGEIPAIIESKDRTKAGITAP 229

Query: 3578 SNGLYLCEVNY 3610
              GLYL  + Y
Sbjct: 230  PQGLYLVRIVY 240



>gi|16801808|ref|NP_472076.1|   highly similar to pseudouridylate synthase I [Listeria innocua]
 gi|24212565|sp|Q927P1|TRUA_LISIN   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|25292043|pir||AE1775   pseudouridylate synthase I homolog truA [imported] - Listeria innocua
            (strain Clip11262)
 gi|16415283|emb|CAC97973.1|   truA [Listeria innocua]
          Length = 248

 Score =  139 bits (349), Expect = 3e-31
 Identities = 88/254 (34%), Positives = 130/254 (51%), Gaps = 1/254 (0%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK I+ Y G+ + G+Q QP+T +T+Q ++EKAL+K+ K   +    SGRTD+GVHA GQV
Sbjct: 4    YKAIISYDGSGFFGYQVQPNT-RTVQAEIEKALEKMHKGKSVRITASGRTDTGVHAKGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +     L++      KAL    P DI  +  E +   F+  F    K Y+Y+       +
Sbjct: 63   IHFDSELDITAEKFQKALQVMTPFDISFLTVEEAPADFHARFGTVGKEYRYVIKRTKIFD 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
                +        +DI KM++A E  IGEHDF  F +  T+  S VR +Y    + E   
Sbjct: 123  PFSRNFALHYPYELDIAKMKQASERLIGEHDFTSFCSARTERDSKVRTLYSIDFYEED-- 180

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKL-AA 3568
                    E  +   +G+GFL  MVR++ GTL + G G++   D+  AL +    KL + 
Sbjct: 181  -------AETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDITKALLAHDRQKLISK 233

Query: 3569 VAPSNGLYLCEVNY 3610
             AP  GLYL  V+Y
Sbjct: 234  TAPPQGLYLWRVDY 247



>gi|21911175|ref|NP_665443.1|   putative tRNA pseudouridine synthase A [Streptococcus pyogenes
            MGAS315]
 gi|28895139|ref|NP_801489.1|   putative tRNA pseudouridine synthase A [Streptococcus pyogenes SSI-1]
 gi|25453306|sp|Q8K5W2|TRUA_STRP3   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|21905386|gb|AAM80246.1|   putative tRNA pseudouridine synthase A [Streptococcus pyogenes
            MGAS315]
 gi|28810384|dbj|BAC63322.1|   putative tRNA pseudouridine synthase A [Streptococcus pyogenes SSI-1]
          Length = 249

 Score =  138 bits (348), Expect = 4e-31
 Identities = 85/253 (33%), Positives = 137/253 (54%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK  + Y GT + G+Q+Q H  +T+Q ++EK L K++   +I   G+GRTD+GVHA GQV
Sbjct: 4    YKATISYDGTLFSGFQRQRHL-RTVQEEIEKTLYKLNNGTKIIIHGAGRTDAGVHAYGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +   +P E E   L  AL++  P DI+ ++ E  ++ F+  +    KTY++L      +N
Sbjct: 63   IHFDLPQEQEVEKLRFALDTQTPEDIDVVNIEKVADDFHCRYQKHLKTYEFLVDNGRPKN 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             ++    T     ++I+ M++A    +G HDF  F   GT + + VR I    +  +++ 
Sbjct: 123  PMMRHYTTHYPYTLNIKLMQDAINGLVGTHDFTGFTAAGTSVQNKVRTITKATVSRDEKT 182

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
             FL        +F   G+GFL + VR MVGTL  IG G++ +  +K+ L+S +       
Sbjct: 183  DFL--------VFTFSGNGFLYKQVRNMVGTLLKIGNGQMPVEQVKVILSSKNRQLAGPT 234

Query: 3572 APSNGLYLCEVNY 3610
               NGLYL E+ Y
Sbjct: 235  ISGNGLYLKEICY 247



>gi|15903494|ref|NP_359044.1|   tRNA pseudouridine synthase A [Streptococcus pneumoniae R6]
 gi|38258775|sp|Q8CWQ1|TRUA_STRR6   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|25292040|pir||B98053   pseudouridylate synthase (EC 4.2.1.70) [imported] - Streptococcus
            pneumoniae (strain R6)
 gi|15459107|gb|AAL00255.1|   tRNA pseudouridine synthase A [Streptococcus pneumoniae R6]
          Length = 249

 Score =  137 bits (345), Expect = 8e-31
 Identities = 83/253 (32%), Positives = 133/253 (52%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK  + Y G  + G+Q+Q H ++++Q ++EK L +++K   I   G+GRTDSGVHALGQV
Sbjct: 4    YKATISYDGYAFAGFQRQSH-ARSVQEEIEKTLTRLNKGQTITVHGAGRTDSGVHALGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +   +P +++   L  AL++  P DI+ I  E  ++ F+  +    KTY+++      +N
Sbjct: 63   IHFDLPYQMDEEKLRFALDTQSPEDIDVISIELVADDFHCRYAKHSKTYEFIVDRGRPKN 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             +     T    P+D+E+M+ A +   G HDF  F   GT +   VR I +  L +++  
Sbjct: 123  PMRRHYATHFPYPLDVERMQIAIKKLEGTHDFTGFTASGTSVEDKVRTITEASLIVDETG 182

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
             FL         F   G+GFL + +R MVGTL  IG  ++ +  + + L           
Sbjct: 183  QFL--------TFTFSGNGFLYKQIRNMVGTLLKIGNNRMPVEQIDLILEKKDRQLAGPT 234

Query: 3572 APSNGLYLCEVNY 3610
            A  NGLYL E+ Y
Sbjct: 235  AAPNGLYLKEIRY 247



>gi|15896350|ref|NP_349699.1|   Pseudouridylate synthase, TRUA [Clostridium acetobutylicum]
 gi|30913407|sp|Q97EL1|TRUA_CLOAB   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|25292037|pir||D97281   pseudouridylate synthase, TRUA [imported] - Clostridium
            acetobutylicum
 gi|15026164|gb|AAK81039.1|   Pseudouridylate synthase, TRUA [Clostridium acetobutylicum]
          Length = 244

 Score =  137 bits (345), Expect = 8e-31
 Identities = 87/252 (34%), Positives = 131/252 (51%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K+ L Y GT Y GWQKQ +   T+Q ++EK + +I+  ++I  IG  RTDSGVHA     
Sbjct: 5    KLTLEYDGTNYCGWQKQKNVV-TVQEEVEKIIGEIT-GEKIDVIGCSRTDSGVHAKAYTC 62

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
              +    + P      LNS LP+DI  ++SE     F+  FD K KTY Y      +R A
Sbjct: 63   NFKTNTVIPPEKFYLVLNSVLPDDIVALNSEEVPMDFHSRFDNKGKTYSYTILNRLQRAA 122

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQG 3394
            +  + +      ++ + MREA +  +G HDF  F + G+ + S +R IY+ ++  ++ + 
Sbjct: 123  IDRNYVYQYGHKLNCDLMREATKYILGTHDFTSFKSTGSKVKSNIRTIYEARIVEDENK- 181

Query: 3395 FLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVA 3574
                      IF V G GFL  MVR++VGTL  +G  K+   ++K  + S    K   V 
Sbjct: 182  ---------VIFYVTGDGFLYNMVRIIVGTLLEVGEEKITPLNVKTIVESKDRTKAGRVV 232

Query: 3575 PSNGLYLCEVNY 3610
            P+ GL L +V Y
Sbjct: 233  PAKGLCLEKVMY 244



>gi|16804636|ref|NP_466121.1|   highly similar to pseudouridylate synthase I [Listeria monocytogenes
            EGD-e]
 gi|24212550|sp|Q8Y457|TRUA_LISMO   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|25292044|pir||AF1399   pseudouridylate synthase I homolog truA [imported] - Listeria
            monocytogenes (strain EGD-e)
 gi|16412086|emb|CAD00676.1|   truA [Listeria monocytogenes]
          Length = 248

 Score =  135 bits (341), Expect = 2e-30
 Identities = 87/254 (34%), Positives = 128/254 (50%), Gaps = 1/254 (0%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK I+ Y G+ + G+Q QP+T +T+Q ++EKAL K+ K   +    SGRTD+GVHA GQV
Sbjct: 4    YKAIISYDGSGFYGYQVQPNT-RTVQAEIEKALTKMHKGKTVRVTASGRTDTGVHAKGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +     L++      KAL    P DI  +  E   + F+  F    K Y+Y+       +
Sbjct: 63   IHFDSELDITAEKFQKALQVMTPFDISFLTVEEVPDDFHARFGTVGKEYRYVVKRTKIFD 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
                +        +DI KM+ A +  IGEHDF  F +  T+  S VR +Y    + E   
Sbjct: 123  PFSRNFALHYPYELDISKMKLASKRLIGEHDFTSFCSARTERDSKVRTLYSIDFYEEDD- 181

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKL-AA 3568
                    E  +   +G+GFL  MVR++ GTL + G G++   D+  AL +    KL + 
Sbjct: 182  --------ETLVIAFQGNGFLYNMVRILTGTLLDAGQGRISPDDISEALLARDRQKLISK 233

Query: 3569 VAPSNGLYLCEVNY 3610
             AP  GLYL  V+Y
Sbjct: 234  TAPPQGLYLWRVDY 247



>gi|28211488|ref|NP_782432.1|   tRNA pseudouridine synthase A [Clostridium tetani E88]
 gi|28203929|gb|AAO36369.1|   tRNA pseudouridine synthase A [Clostridium tetani E88]
          Length = 245

 Score =  134 bits (338), Expect = 5e-30
 Identities = 84/252 (33%), Positives = 129/252 (51%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K+IL Y GT+Y+GWQKQ     TIQ ++E  L K++  D I  IG GRTD+GVHA   V 
Sbjct: 5    KMILEYDGTRYKGWQKQKKDVLTIQDKIETVLSKMTGED-IQVIGCGRTDAGVHAENYVA 63

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
                  +     +L  L   LP DI     +++SE F+  ++ K KTY Y  + N  R+ 
Sbjct: 64   NFHTNCDFTVDYMLDYLYEFLPEDIVVKTMKDTSERFHARYNVKSKTYVYRINNNKFRSV 123

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQG 3394
                     +  ++I  M++A E  IG HDF  F  + ++  ST+R I    +++ + QG
Sbjct: 124  FNKKYAYHDNEKLNISAMKDAAEFLIGTHDFKSFTRLKSNSKSTIRAIK--YINITENQG 181

Query: 3395 FLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVA 3574
             +          EV G+GFL  MVR++ G L  +G   ++  D++  LN    A  + + 
Sbjct: 182  IIS--------IEVNGNGFLLNMVRIVAGALLEVGKENIKPIDIEKMLNEKKRADASLIL 233

Query: 3575 PSNGLYLCEVNY 3610
            P+ GL L ++ Y
Sbjct: 234  PAKGLCLKDIQY 245



>gi|22993077|ref|ZP_00037688.1|   COG0101: Pseudouridylate synthase [Enterococcus faecium]
          Length = 246

 Score =  134 bits (337), Expect = 7e-30
 Identities = 85/252 (33%), Positives = 130/252 (51%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K+ + Y G +Y GWQ+     +TIQG++EK L +++ ++EI  IGSGRTD+G HA GQV 
Sbjct: 5    KLTIEYDGKRYSGWQRLGDDDKTIQGKIEKVLHQMT-NEEIEIIGSGRTDAGTHARGQVA 63

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
              +   E+    ++  +N +LP DI     E   E F+  ++A  K Y Y    N   +A
Sbjct: 64   NFKTNTEIGLAEMIDFMNRYLPRDIVIKRIEEMPERFHSRYNAVGKKYSYYVWNNVIPSA 123

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQG 3394
               +      + +D++K+  ACE  +G HDF  F  +     STVR I +  L +E++  
Sbjct: 124  FERNHSFYFPQELDMDKLNAACEKLVGTHDFIGFSALKKSKKSTVRTIDE--LSIERKGE 181

Query: 3395 FLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVA 3574
             L      H+ F   G GFL +MVR+++GTL  IG G + +  +     S          
Sbjct: 182  ML------HFTF--VGDGFLYKMVRIIMGTLLEIGTGAMPIETIDEIFESKVRQHAGETV 233

Query: 3575 PSNGLYLCEVNY 3610
            P+ GL+L EV Y
Sbjct: 234  PAQGLFLDEVYY 245



>gi|15612730|ref|NP_241033.1|   tRNA pseudouridine synthase A (pseudouridylate synthase I) [Bacillus
            halodurans]
 gi|8134764|sp|Q9Z9J0|TRUA_BACHD   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|11269487|pir||T44415   tRNA pseudouridine synthase A (pseudouridylate synthase I) truA
            [imported] - Bacillus halodurans (strain C-125)
 gi|4512436|dbj|BAA75303.1|   truA homologue (identity of 62% to B. subtilis ) [Bacillus
            halodurans]
 gi|10172779|dbj|BAB03886.1|   tRNA pseudouridine synthase A (pseudouridylate synthase I) [Bacillus
            halodurans]
          Length = 263

 Score =  133 bits (335), Expect = 1e-29
 Identities = 83/240 (34%), Positives = 119/240 (49%)
 Frame = +2

Query: 2870 YKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVVRVQIP 3049
            Y GT + G+Q QP+  +T+QG+LE  LK I K   I    SGRTD+GVHA GQ+V     
Sbjct: 10   YDGTDFAGYQIQPN-ERTVQGELESVLKNIHKGMSIRVTASGRTDTGVHARGQIVHFDTS 68

Query: 3050 LELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNALVDDS 3229
            L         ALNS LP DI  + + +    F+  + AK K Y+Y    + + +    + 
Sbjct: 69   LSFPVDRWPIALNSQLPADICVLEAADVPADFHARYSAKTKEYRYRVLTSAQADVFRRNY 128

Query: 3230 MTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGFLGEV 3409
               +  P+D+E M+ A    +G HDF+ F     ++   VR I D  L  E         
Sbjct: 129  TYHVRYPLDVEAMQRAAVQLLGTHDFSSFCAAKAEVEDKVRTIEDVALWRE--------- 179

Query: 3410 YPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAPSNGL 3589
              +  IF ++G+GFL  MVR++VGTL  IG GK    ++   L + S       AP +GL
Sbjct: 180  -GDELIFSIRGNGFLYNMVRIIVGTLLEIGAGKRSAEEVAKILAARSREAAGKTAPGHGL 238



>gi|30018678|ref|NP_830309.1|   tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|29894219|gb|AAP07510.1|   tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
          Length = 245

 Score =  133 bits (334), Expect = 2e-29
 Identities = 79/253 (31%), Positives = 132/253 (52%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK+ ++Y G +++GWQ+  +   TIQG++E  + ++    EI  IG  RTD+GVHAL QV
Sbjct: 4    YKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMV-GKEIEIIGCSRTDAGVHALNQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
               Q   +L    + K LN +LPNDI   + E   + F+  +++K KTY Y        N
Sbjct: 63   ANFQSDEKLVEHKVKKYLNQYLPNDISITNVEEVHDRFHARYNSKAKTYLYKIWNEEHTN 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
              +      +++ ++++ M+ A +  +G HDF  F    +   S VR +Y   L + ++ 
Sbjct: 123  PFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVY--TLDVMEEA 180

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
            GF+           V G+GFL  MVR +VG L  +GLG+++   +   L      ++  +
Sbjct: 181  GFVQ--------IRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCL 232

Query: 3572 APSNGLYLCEVNY 3610
            A ++GLYL  V +
Sbjct: 233  AEASGLYLENVEF 245



>gi|28212149|ref|NP_783093.1|   tRNA pseudouridine synthase A [Clostridium tetani E88]
 gi|38258761|sp|Q890R5|TRUA_CLOTE   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|28204593|gb|AAO37030.1|   tRNA pseudouridine synthase A [Clostridium tetani E88]
          Length = 248

 Score =  131 bits (330), Expect = 4e-29
 Identities = 86/253 (33%), Positives = 128/253 (50%), Gaps = 1/253 (0%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTS-QTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            ++ + Y GT Y GWQKQ   + +TIQ  +EKA+++ +K +E+  IGS RTD+GVHAL   
Sbjct: 6    RLKVEYDGTNYSGWQKQKDKNIKTIQSSIEKAIEEATK-EEVELIGSSRTDAGVHALAYT 64

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
               +    +       ALN  LP DI  + SE     F+  FD   KTY Y        +
Sbjct: 65   ANFKTCSTIPGEKFKHALNRFLPEDIVILESEEVPMEFHSRFDCIGKTYVYKILNRPLFS 124

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             +  + +  +   +DI  M EA +  IG HDF  F   G ++ +TVR I +  +    + 
Sbjct: 125  PIQRNYIYHVKDELDINSMIEASKFLIGTHDFNAFKKSGGNLKTTVRTITNINI---LKS 181

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
              + E++       V G GFL  MVR++ GTL  +GL + +  D+ + L S    K    
Sbjct: 182  NDIVEIH-------VSGDGFLYNMVRIISGTLIEVGLSRRKPEDISIILQSKDRCKAGMC 234

Query: 3572 APSNGLYLCEVNY 3610
            AP+ GLYL E+ Y
Sbjct: 235  APARGLYLKELFY 247



>gi|13358100|ref|NP_078374.1|   pseudouridylate synthase I [Ureaplasma urealyticum]
 gi|26006901|sp|Q9PPV4|TRUA_UREPA   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|11269468|pir||B82879   pseudouridylate synthase I UU536 [imported] - Ureaplasma urealyticum
 gi|6899540|gb|AAF30949.1|   pseudouridylate synthase I [Ureaplasma urealyticum]
          Length = 241

 Score =  131 bits (329), Expect = 6e-29
 Identities = 85/254 (33%), Positives = 138/254 (54%), Gaps = 1/254 (0%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YKI LRY G+ + GW +QP   +T+QG LE+  K I K + I  IGSGRTD GVHA  Q 
Sbjct: 3    YKISLRYDGSLFYGWARQPQ-KRTVQGDLEEIFKSIFKINNIRIIGSGRTDKGVHAYEQT 61

Query: 3032 VRVQ-IPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRR 3208
              V+   L+ +   + +AL S   +DI+ +  +   + F+  ++A  KTY+Y+ + +   
Sbjct: 62   FSVKHSALKYDSHIIYQALCSRTSSDIQILEVQKVDDSFHAQYNATSKTYQYVIN-DYEF 120

Query: 3209 NALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQ 3388
            +   ++    +++ ++ +K+ EA ELF+GEHDF  F T  ++++ T+R I   K+  +  
Sbjct: 121  DLFRNNYELFVNQKINDQKILEALELFVGEHDFKSFST--SELTMTIRRINWVKIKRD-- 176

Query: 3389 QGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAA 3568
                      H I  +  +GFLK MVR++V +  +    K+ LA +   L  P       
Sbjct: 177  ---------THLIIYINANGFLKNMVRMIVASCLDYAFNKISLAKIHELLIYPKKGASIK 227

Query: 3569 VAPSNGLYLCEVNY 3610
            +AP+ GLYL +V Y
Sbjct: 228  LAPACGLYLYKVYY 241



>gi|23024296|ref|ZP_00063512.1|   COG0101: Pseudouridylate synthase [Leuconostoc mesenteroides subsp.
            mesenteroides ATCC 8293]
          Length = 255

 Score =  130 bits (328), Expect = 8e-29
 Identities = 80/259 (30%), Positives = 135/259 (52%), Gaps = 6/259 (2%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTS----QTIQGQLEKALKKISK--SDEIHTIGSGRTDSGV 3013
            YK ++ Y G ++ G+Q Q        +T+QG+L K + K++K  S +I  +G+ RTD+GV
Sbjct: 4    YKAVIAYDGAEFFGFQLQTKNGVESVRTVQGELNKVINKMAKNPSPQIKVVGASRTDTGV 63

Query: 3014 HALGQVVRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFS 3193
            HA GQVV   +P  ++P  + K +N+ LP D+   H E+ S+ F+  F+   K Y Y  S
Sbjct: 64   HAFGQVVHFDLPFNIDPEGVRKGMNTLLPFDVVVNHVEHVSDDFHARFNTHSKRYIYRVS 123

Query: 3194 LNGRRNALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKL 3373
                ++             +DI +++ A    +GEHDFA F   G + ++T+R+I    +
Sbjct: 124  TTDYKDPFKRKYTGHFHWKLDINRIKAALPDLLGEHDFASFAASGNETATTIRLITRADV 183

Query: 3374 HLEKQQGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSG 3553
              + ++           +F  +G+ FL   +R+MVG L  IG GK  + D+   +     
Sbjct: 184  DEKPEE--------HEIVFTFEGNAFLYNQIRIMVGVLLEIGTGKRPVHDIVRLIEVKDR 235

Query: 3554 AKLAAVAPSNGLYLCEVNY 3610
             +    AP++GLYL E++Y
Sbjct: 236  EQARYTAPASGLYLDEIDY 254



>gi|16077216|ref|NP_388029.1|   pseudouridylate synthase I [Bacillus subtilis]
 gi|3915172|sp|P70973|TRUA_BACSU   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|7437066|pir||F69726   pseudouridylate synthase I truA - Bacillus subtilis
 gi|1644206|dbj|BAA10987.1|   unknown [Bacillus subtilis]
 gi|2632415|emb|CAB11924.1|   pseudouridylate synthase I [Bacillus subtilis subsp. subtilis str.
            168]
          Length = 247

 Score =  129 bits (325), Expect = 2e-28
 Identities = 88/253 (34%), Positives = 124/253 (49%), Gaps = 1/253 (0%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKS-DEIHTIGSGRTDSGVHALGQV 3031
            K  + Y G  + G+Q QP   +T+Q +LEKAL  + KS D I  + SGRTDSGVHA GQV
Sbjct: 4    KCTISYDGHLFNGYQVQPG-KRTVQDELEKALAVLHKSKDRIPVVSSGRTDSGVHAAGQV 62

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            +    PL +       ALN+ LP+DI    +E + + F+  F A  K Y+Y        +
Sbjct: 63   IHFDTPLSIPAERWPYALNALLPDDIAVKQAEIADDGFHARFSAVKKEYRYFVYTEKHPD 122

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
                         ++++ MREA +  IG HDF  F    T++   VR IY+     E   
Sbjct: 123  VFKRHYAYHFSYRLNVQDMREAAKHPIGTHDFTSFCAAKTEVQDKVRTIYELDW-TETAD 181

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
            G             + GSGFL  MVR++ GTL + G+GK+   ++K  L +         
Sbjct: 182  GLQ---------MRITGSGFLYNMVRIIAGTLLDAGIGKISPDEVKSMLEAKDREAAERT 232

Query: 3572 APSNGLYLCEVNY 3610
            AP +GLYL  V Y
Sbjct: 233  APGHGLYLWNVYY 245



>gi|23003456|ref|ZP_00047118.1|   COG0101: Pseudouridylate synthase [Lactobacillus gasseri]
          Length = 264

 Score =  129 bits (324), Expect = 2e-28
 Identities = 87/254 (34%), Positives = 131/254 (51%), Gaps = 1/254 (0%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK+ + Y G  + G+Q QP+  +T+QG +E+ALKK++K   +   GSGRTD+GVHA GQV
Sbjct: 6    YKLTMAYDGHLFHGFQIQPN-ERTVQGVIEEALKKMTKGKRVVVHGSGRTDAGVHAKGQV 64

Query: 3032 VRVQI-PLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRR 3208
            +       E+   +++ ALN+ +P D     SE     F+  +  K K Y+Y+   +   
Sbjct: 65   IHFDYPGKEIPAKNMMLALNALMPIDTVFFDSEIVDSDFHVQYSTKGKWYRYIVDQHRFT 124

Query: 3209 NALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQ 3388
            +            P+DI  M++A +  IGEHDF  F   G  I   VR IY   +  +  
Sbjct: 125  DPFNRFYTGHYPYPLDIALMKKAAKDLIGEHDFTSFAASGGQIVDKVRTIYYVNITSDPD 184

Query: 3389 QGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAA 3568
                     +  IF+  G+GFL  MVR++VGTL  IG  K  + D+   L +    ++  
Sbjct: 185  N--------KKIIFDFIGNGFLYNMVRILVGTLLEIGNKKRPVDDIPRVLAAKDRQEVRT 236

Query: 3569 VAPSNGLYLCEVNY 3610
             AP++GLYL  V Y
Sbjct: 237  TAPASGLYLQHVFY 250



>gi|23097605|ref|NP_691071.1|   tRNA pseudouridine synthase A [Oceanobacillus iheyensis HTE831]
 gi|38258776|sp|Q8CXP1|TRUA_OCEIH   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|22775828|dbj|BAC12106.1|   tRNA pseudouridine synthase A [Oceanobacillus iheyensis HTE831]
          Length = 253

 Score =  129 bits (324), Expect = 2e-28
 Identities = 88/253 (34%), Positives = 129/253 (50%), Gaps = 1/253 (0%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K  + Y G+ + G+Q QP   +T+QG LEKAL  + K   I    SGRTD+GVHA+GQV+
Sbjct: 5    KCTVSYDGSDFAGFQVQPD-HRTVQGVLEKALYNMHKGKSIRIQASGRTDTGVHAVGQVI 63

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
                PLE+   +  +ALN+ LP+D+     E  +E F+  +  K+K Y Y        N 
Sbjct: 64   HFDSPLEIPERNWKQALNTLLPDDVRIQKVEKKTEEFHARYSVKEKEYHYFVLNEEDPNV 123

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDI-SSTVRVIYDCKLHLEKQQ 3391
                 +    R +D+E+M+EAC+   G HDF  F +  + +  S VR +Y    H   Q 
Sbjct: 124  FQRGYVYHEPRKLDLERMQEACQYLEGTHDFTSFSSAKSSVKGSKVRTLYHVSCH---QT 180

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
            G        +  F  +GSGFL  MVR+M+  L ++G GK    D+   L S +  ++   
Sbjct: 181  G-------TNIEFIFRGSGFLYNMVRIMMSVLIDVGKGKRNPEDIIDLLASKNRQQIGKT 233

Query: 3572 APSNGLYLCEVNY 3610
                GLYL  V+Y
Sbjct: 234  MAPQGLYLWRVSY 246



>gi|37527059|ref|NP_930403.1|   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase) (PSU-I)
            [Photorhabdus luminescens subsp. laumondii TTO1]
 gi|36786492|emb|CAE15547.1|   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase) (PSU-I)
            [Photorhabdus luminescens subsp. laumondii TTO1]
          Length = 279

 Score =  126 bits (317), Expect = 1e-27
 Identities = 77/249 (30%), Positives = 131/249 (52%)
 Frame = +2

Query: 2864 LRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVVRVQ 3043
            + Y G++Y GWQ+Q    +++QG LE+AL K++  + I    +GRTD+GVHA GQVV  +
Sbjct: 22   IEYDGSRYYGWQRQQEV-KSVQGCLEEALSKVA-DEPISVFCAGRTDAGVHATGQVVHFE 79

Query: 3044 IPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNALVD 3223
              ++ +  +    +N HLP DI     +   E F+  F A  + Y+Y+   +  R A++ 
Sbjct: 80   TSVQRKDAAWTMGVNVHLPPDIAVRWVKTVDEGFHARFSATARRYRYIIFNHRYRPAVLA 139

Query: 3224 DSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGFLG 3403
            + +T    P+D ++M +A +  +GE+DF  F  V     +  R +    +H+   +    
Sbjct: 140  NGVTHFHYPLDEKRMHQAAQCILGENDFTSFRAVQCQSKTPWRNV----MHINVNR---- 191

Query: 3404 EVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAPSN 3583
              Y  + + ++K + F+  MVR + G+L  IG G  ++  +   L     AK AA A + 
Sbjct: 192  --YGHYVVIDIKANAFVHHMVRNIAGSLMEIGCGNQDINWMAQLLALKDRAKAAATAKAA 249

Query: 3584 GLYLCEVNY 3610
            GLYL  V+Y
Sbjct: 250  GLYLVAVDY 258



>gi|15672468|ref|NP_266642.1|   tRNA pseudouridine synthase A [Lactococcus lactis subsp. lactis]
 gi|13878837|sp|Q9CI80|TRUA_LACLA   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|25292032|pir||F86685   pseudouridylate synthase (EC 4.2.1.70) [imported] - Lactococcus
            lactis subsp. lactis (strain IL1403)
 gi|12723367|gb|AAK04584.1|   tRNA pseudouridine synthase A (EC 4.2.1.70) [Lactococcus lactis
            subsp. lactis]
          Length = 253

 Score =  126 bits (317), Expect = 1e-27
 Identities = 82/254 (32%), Positives = 130/254 (51%), Gaps = 1/254 (0%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YK  + Y GT + G+Q Q +  +T+Q ++EK L K++  + +   GSGRTDSGVHA GQV
Sbjct: 4    YKATIAYDGTDFAGFQSQTN-QRTVQKEIEKILTKLNSFEPVILQGSGRTDSGVHAFGQV 62

Query: 3032 VRVQIPLELEPLSLLK-ALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRR 3208
            +   +  ++  L  L+  L++  P DI     E   + ++  +   +KTY+Y    +  R
Sbjct: 63   IHFDLKGKVRDLERLRFGLDTQTPADIAVKKVELVPDDWHARYQKHEKTYEYYLENSITR 122

Query: 3209 NALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQ 3388
            +     S      P++ E+M+EA    +GEHDF  F   G+ +   VR IY         
Sbjct: 123  SPFQRHSKAYFRYPLNFERMQEAMSKLVGEHDFTGFTASGSSVDDKVRTIY--------- 173

Query: 3389 QGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAA 3568
            Q  +  +  E++ F  +G+GFL + VR MVGT+  IG  ++ ++ +   L S +      
Sbjct: 174  QAEIIRLDEENFKFIFRGNGFLYKQVRNMVGTVIKIGNDRMPVSQIDKILTSKNRDFAGP 233

Query: 3569 VAPSNGLYLCEVNY 3610
             A   GLYL EV Y
Sbjct: 234  TAAPEGLYLKEVKY 247



>gi|39997968|ref|NP_953919.1|   tRNA pseudouridine synthase A [Geobacter sulfurreducens PCA]
 gi|39984913|gb|AAR36269.1|   tRNA pseudouridine synthase A [Geobacter sulfurreducens PCA]
          Length = 244

 Score =  126 bits (316), Expect = 2e-27
 Identities = 86/252 (34%), Positives = 122/252 (48%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVV 3034
            K+IL Y GT Y GWQ QP+   +IQ  +E AL ++ K + +    SGRTD+GVHA G V 
Sbjct: 5    KLILEYDGTNYAGWQLQPN-GLSIQEVVEGALARLLK-EPVRLRASGRTDAGVHARGMVA 62

Query: 3035 RVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNA 3214
                   +   +    LN+ LP DI    ++ +   FNP F A  K Y+Y      RR+ 
Sbjct: 63   AFDTDRSIPLRAFSDGLNALLPPDIAVRSADEALPGFNPRFAATGKHYRYTIHRGERRSP 122

Query: 3215 LVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQG 3394
            LV      +   +++  MREA     GE DFA F T G    +T+R +   ++  +    
Sbjct: 123  LVRLQSWHVRGALNLAAMREAARHLTGERDFASFRTAGCAARTTIRRVDAVEISDD---- 178

Query: 3395 FLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVA 3574
                   E    +V GSGFL+ MVR+MVGTL  +G GK+    +   +  P        A
Sbjct: 179  ------GEMLTVDVHGSGFLRNMVRIMVGTLVEVGRGKLTPEHVAQMVVCPGVVPAGPTA 232

Query: 3575 PSNGLYLCEVNY 3610
            P  GL L +V +
Sbjct: 233  PPQGLCLQKVRF 244



>gi|33519947|ref|NP_878779.1|   tRNA pseudouridine synthase A [Candidatus Blochmannia floridanus]
 gi|33504293|emb|CAD83185.1|   tRNA pseudouridine synthase A [Candidatus Blochmannia floridanus]
          Length = 252

 Score =  126 bits (316), Expect = 2e-27
 Identities = 87/250 (34%), Positives = 130/250 (52%), Gaps = 1/250 (0%)
 Frame = +2

Query: 2864 LRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVVRVQ 3043
            + Y G+ Y GWQKQ   S +IQ  LE AL K+S S+ I     GRTDSGVHAL Q+V  +
Sbjct: 8    VEYDGSMYCGWQKQKCVS-SIQSCLEYALSKVS-SESILVFCGGRTDSGVHALEQIVHFE 65

Query: 3044 IPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNALVD 3223
              L+    +    +N HLPNDI           F+  F A  + Y Y    N  R+A+  
Sbjct: 66   TQLKCSRSAWTLGVNCHLPNDICVRWVSEVDNSFHARFSAISRRYCYFIYNNRIRSAVFC 125

Query: 3224 DSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGFLG 3403
              +    R +D+ KM +A +  +GE+DF+ F + G+   ST R IY  ++    +QG   
Sbjct: 126  KRVWSYSRFLDVNKMSKAAQYLLGENDFSVFRSSGSQSCSTNRNIYHLRVI---RQG--- 179

Query: 3404 EVYPEHYI-FEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAPS 3580
                 HY+  +++ + FL +MVR +VG+L  +G G   +  +   L +  G+     AP+
Sbjct: 180  -----HYVVIDIRANAFLYRMVRNIVGSLVEVGCGNKPVTWILELLKNYRGSLNRITAPA 234

Query: 3581 NGLYLCEVNY 3610
            +GLYL E+ Y
Sbjct: 235  SGLYLVEIKY 244



>gi|15677859|ref|NP_275027.1|   tRNA pseudouridine synthase A [Neisseria meningitidis MC58]
 gi|25009507|sp|Q9JXI2|TRUA_NEIMB   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|11269478|pir||A81014   tRNA pseudouridine synthase A NMB2036 [imported] - Neisseria
            meningitidis (strain MC58 serogroup B)
 gi|7227297|gb|AAF42357.1|   tRNA pseudouridine synthase A [Neisseria meningitidis MC58]
          Length = 265

 Score =  125 bits (314), Expect = 3e-27
 Identities = 78/253 (30%), Positives = 124/253 (49%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            + I L Y G+++ GWQKQ     T+Q  LE AL +I+  + + T  +GRTD+GVHA  QV
Sbjct: 9    WAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIA-GEAVSTTVAGRTDTGVHATAQV 67

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            V           + ++ +N+HLP  I  +H+   +  F+  FDA  + Y+YL      R+
Sbjct: 68   VHFDTTAARPQQAWVRGVNAHLPEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPVRS 127

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             L+ +        +DI +MR+A  L +GE DF+ F        S V+ IY  +  L +  
Sbjct: 128  PLLKNRAGWTHLKLDIGQMRQAAALLVGEQDFSSFRAAECQAKSPVKTIY--RADLTQSS 185

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
            G +          ++ G+ FL  MVR ++G L  +G G++ +      +   S  K    
Sbjct: 186  GLVR--------LDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPT 237

Query: 3572 APSNGLYLCEVNY 3610
               +GLYL  V+Y
Sbjct: 238  FMPDGLYLTGVDY 250



>gi|13431951|sp|Q9PJT0|TRUA_CHLMU   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|11269474|pir||D81669   tRNA pseudouridine synthase A TC0748 [imported] - Chlamydia muridarum
            (strain Nigg)
          Length = 267

 Score =  125 bits (314), Expect = 3e-27
 Identities = 105/263 (39%), Positives = 136/263 (51%), Gaps = 8/263 (3%)
 Frame = +2

Query: 2855 KIILR--YKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQ 3028
            KIILR  Y+GT Y GWQ QP+ + +IQ  LE  L+KIS++  I  I SGRTD+GVHA GQ
Sbjct: 4    KIILRIAYQGTAYSGWQYQPN-ALSIQEVLETLLQKISRT-RISVIASGRTDAGVHAQGQ 61

Query: 3029 VVRV---QIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLN 3199
            V        P   +P  + K LN+ LP+DI       ++E F+  F A  K Y Y  SL 
Sbjct: 62   VAHFCCPDHPHFSDPGQIKKMLNALLPHDIVIRDVIATNEDFHSRFSAITKEYHYTLSLL 121

Query: 3200 GRRNALVDDSMTCLD--RPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKL 3373
             +   L    + C      + +E MREA +  +G HDFA F  +G + SSTVR +Y   L
Sbjct: 122  PK--PLPHHRLFCFSPRHKLCLESMREAAKYLVGTHDFASFANLGREYSSTVRTLYALDL 179

Query: 3374 HLEKQQGFLGEVYPEHYIFEV-KGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPS 3550
             LE+          EH +  + KG+GFL +MVR +VG L +IG GK     L   L    
Sbjct: 180  -LEQ----------EHLVTVICKGNGFLYKMVRNIVGALLDIGKGKYPPEHLLEMLEKKD 228

Query: 3551 GAKLAAVAPSNGLYLCEVNY*MP 3619
              K    AP  GL L  V Y  P
Sbjct: 229  RKKGPPSAPPYGLSLHHVCYPSP 251



>gi|15793409|ref|NP_283231.1|   tRNA pseudouridine synthase [Neisseria meningitidis Z2491]
 gi|25009506|sp|Q9JWF1|TRUA_NEIMA   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|11269475|pir||G81956   pseudouridylate synthase (EC 4.2.1.70) tRNA-specific NMA0402
            [imported] - Neisseria meningitidis (strain Z2491
            serogroup A)
 gi|7379154|emb|CAB83702.1|   tRNA pseudouridine synthase [Neisseria meningitidis Z2491]
          Length = 265

 Score =  124 bits (312), Expect = 5e-27
 Identities = 79/253 (31%), Positives = 122/253 (48%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            + I L Y G+++ GWQKQ     T+Q  LE AL +I+  + + T  +GRTD+GVHA  QV
Sbjct: 9    WAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIA-GEAVSTTVAGRTDTGVHATAQV 67

Query: 3032 VRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRN 3211
            V           + ++ +N+HLP  I  +H+   +  F+  FDA  + Y+YL      R+
Sbjct: 68   VHFDTTAARPQQAWVRGVNAHLPEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPVRS 127

Query: 3212 ALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQ 3391
             L+ +        +DIE MR A    IGE DF+ F        S V+ IY  +  L +  
Sbjct: 128  PLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIY--RADLTQSA 185

Query: 3392 GFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAV 3571
            G +          ++ G+ FL  MVR ++G L  +G G++ +      +   S  K    
Sbjct: 186  GLVR--------LDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPT 237

Query: 3572 APSNGLYLCEVNY 3610
               +GLYL  V+Y
Sbjct: 238  FMPDGLYLTGVDY 250



>gi|23473971|ref|ZP_00129266.1|   COG0101: Pseudouridylate synthase [Desulfovibrio desulfuricans G20]
          Length = 278

 Score =  124 bits (310), Expect = 9e-27
 Identities = 90/270 (33%), Positives = 126/270 (46%), Gaps = 18/270 (6%)
 Frame = +2

Query: 2855 KIILRYKGTQYQGWQKQ------PHTSQ--TIQGQLEKALKKISKSDEIHTIGSGRTDSG 3010
            K+I+ Y GT+Y GWQ Q      PH  Q  T+Q  +E A K I  S  +   G+GRTDSG
Sbjct: 5    KLIIAYAGTRYAGWQIQCLPAGRPHAVQQPTVQQAVEDAAKAILGS-AVRVHGAGRTDSG 63

Query: 3011 VHALGQVVRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLF 3190
            VHA GQV  + IP     +   +ALN+ LP DI  + +    + F+  FDA  K Y Y  
Sbjct: 64   VHAEGQVAHLDIPDAKAAVDWRRALNAKLPEDISVLQAAVVPDGFHARFDAVKKRYTYRI 123

Query: 3191 SLNGRRNALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCK 3370
             L              +  P+DI  M  A     G HDFA F   GT++++TVR +Y   
Sbjct: 124  WLTRAFVLPQRRPFVHMTGPLDIAAMDAAAAFMTGTHDFASFQNAGTELATTVRTVYS-- 181

Query: 3371 LHLEKQQGFLGEVYPEHY----------IFEVKGSGFLKQMVRLMVGTLWNIGLGKVELA 3520
              + +  G   + +P  +           +  +  GFLKQMVR M+G L   G G+    
Sbjct: 182  --ITRTPGLAPDDFPRSHDTTPRAPLELAWHFEADGFLKQMVRNMMGLLLWTGTGRCAPE 239

Query: 3521 DLKMALNSPSGAKLAAVAPSNGLYLCEVNY 3610
            D+   + +      A  AP+ GL +  V Y
Sbjct: 240  DVPAIIAARDRRLSAPTAPACGLTMERVFY 269



>gi|27468710|ref|NP_765347.1|   tRNA pseudouridine synthase A [Staphylococcus epidermidis ATCC 12228]
 gi|32130291|sp|Q8CML6|TRUA_STAEP   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|27316258|gb|AAO05433.1|   tRNA pseudouridine synthase A [Staphylococcus epidermidis ATCC 12228]
          Length = 267

 Score =  123 bits (309), Expect = 1e-26
 Identities = 87/254 (34%), Positives = 125/254 (49%), Gaps = 1/254 (0%)
 Frame = +2

Query: 2864 LRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSD-EIHTIGSGRTDSGVHALGQVVRV 3040
            + Y+G Q+ G+Q Q    +T+Q Q EK LK++ K    IH   S RTD GVHA  Q    
Sbjct: 7    IAYQGNQFLGFQIQQQ-GRTVQQQFEKILKRMHKHHVRIHP--SSRTDRGVHAYQQFFHF 63

Query: 3041 QIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNALV 3220
               L ++      A+N  LP+DI   +  N  E F+  +D   K Y+Y       RN   
Sbjct: 64   DTELNIDNKQWQYAMNRALPDDIYVKNVRNVDEYFHCRYDCVGKRYRYKVYQGNHRNPFK 123

Query: 3221 DDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGFL 3400
              + T ++  +D +KM +A + FIG HDF  F +  T++ S VR +Y  ++   K     
Sbjct: 124  SGTETFVNETLDYDKMNKAAQEFIGTHDFTGFCSQKTEVESKVRTLYQSEIVATK----- 178

Query: 3401 GEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAPS 3580
                 E + + V GSGFL  MVR++V  L  +G GK E  D+   L   +   +   AP 
Sbjct: 179  -----EGFDYVVTGSGFLYNMVRVLVAFLIEVGKGKREPNDVPKLLEDKNRNNVPLTAPP 233

Query: 3581 NGLYLCEVNY*MPE 3622
            +GLYL E  Y  PE
Sbjct: 234  DGLYL-EKIYLSPE 246



>gi|15598310|ref|NP_251804.1|   tRNA-pseudouridine synthase I [Pseudomonas aeruginosa PA01]
 gi|8134770|sp|O87016|TRUA_PSEAE   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|11352726|pir||E83257   tRNA-pseudouridine synthase I PA3114 [imported] - Pseudomonas
            aeruginosa (strain PAO1)
 gi|3237313|gb|AAC23941.1|   HisT [Pseudomonas aeruginosa]
 gi|9949225|gb|AAG06502.1|   tRNA-pseudouridine synthase I [Pseudomonas aeruginosa PAO1]
          Length = 285

 Score =  123 bits (308), Expect = 2e-26
 Identities = 79/249 (31%), Positives = 126/249 (50%)
 Frame = +2

Query: 2864 LRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVVRVQ 3043
            + YKG++Y+GWQ+Q     ++Q  LE+AL K++ ++ +  I +GRTD+ VHA GQVV   
Sbjct: 24   IEYKGSRYRGWQRQEAGVPSVQEALERALSKVA-AEPVGVICAGRTDAAVHASGQVVHFD 82

Query: 3044 IPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNALVD 3223
              +E    + +   N++LP DI    +      F+  F A  + Y+Y    +  R A + 
Sbjct: 83   TAVERPLKAWVMGTNANLPADISVTWARVMPAHFHARFSAMARRYRYAIYNDPIRPAHLA 142

Query: 3224 DSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGFLG 3403
            + +T   RP+DI +MREA ++ +G HDF  F  V     S V+ ++  +L    + G L 
Sbjct: 143  EEVTWNHRPLDIGRMREAAQVLVGTHDFTSFRAVQCQAKSPVKTMHHVRL---LEHGRL- 198

Query: 3404 EVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAPSN 3583
                   + +++G+ FL  MVR + G L  IG G+  +   K  L +         A   
Sbjct: 199  ------IVLDIRGNAFLHHMVRNIAGVLMTIGAGERPIEWAKEVLEARDRRAGGVTAHPY 252

Query: 3584 GLYLCEVNY 3610
            GLYL  V Y
Sbjct: 253  GLYLVRVEY 261



>gi|23062372|ref|ZP_00087161.1|   COG0101: Pseudouridylate synthase [Pseudomonas fluorescens PfO-1]
          Length = 313

 Score =  122 bits (306), Expect = 3e-26
 Identities = 81/256 (31%), Positives = 131/256 (51%), Gaps = 2/256 (0%)
 Frame = +2

Query: 2849 FYKIIL--RYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHAL 3022
            F+++ L   YKG++Y GWQ+Q     T+Q  LEKAL K++ S  I    +GRTD+GVHA 
Sbjct: 45   FFRVALGVEYKGSRYSGWQRQSTGVLTVQETLEKALSKVADSP-ISLQCAGRTDAGVHAC 103

Query: 3023 GQVVRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNG 3202
            GQVV     ++    + +   N +LP+DI    ++     F+  F A  + Y+Y+   + 
Sbjct: 104  GQVVHFDTQVDRSLKAWVMGANINLPHDISVSWAKIMPAHFHARFKAIARRYRYVIYNDQ 163

Query: 3203 RRNALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLE 3382
             R A +++ +T   RP+D+E+M EA +  IG HDF+ F        S ++ ++    HL 
Sbjct: 164  IRPAHLNEEITWNHRPLDVERMAEAAQYLIGTHDFSAFRAGQCQAKSPIKQMH----HLR 219

Query: 3383 KQQGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKL 3562
              +      + +  + +++ + FL  MVR + G L  IG G+  +  +K  L S      
Sbjct: 220  VTR------HGKMIVLDIRANAFLHHMVRNIAGVLMTIGAGERPVEWMKEVLESRERRSG 273

Query: 3563 AAVAPSNGLYLCEVNY 3610
               A   GLYL +V Y
Sbjct: 274  GVTAHPFGLYLVQVEY 289



>gi|27262396|gb|AAN87479.1|   tRNA pseudouridine synthase A [Heliobacillus mobilis]
          Length = 249

 Score =  122 bits (305), Expect = 4e-26
 Identities = 80/249 (32%), Positives = 121/249 (48%), Gaps = 2/249 (0%)
 Frame = +2

Query: 2864 LRYKGTQYQGWQKQ--PHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVVR 3037
            + Y GT Y G+Q Q  P    TIQ +L +A++ ++  +E+    +GRTD+GVHA GQVV 
Sbjct: 1    MSYDGTSYHGFQTQEDPTNLPTIQDELMRAIQVLT-GEEVKITCAGRTDAGVHARGQVVD 59

Query: 3038 VQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNAL 3217
                  +       A+NS LP DI  + +E  +E F+  F A  K Y+Y    +   +  
Sbjct: 60   FLTTSRIPDEKFPLAMNSLLPKDIAVVKAETVAEDFHSRFGALGKHYRYSIYNHRIHSPF 119

Query: 3218 VDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGF 3397
                   +  P+ +  M+EA   F+G HDF  F   G+ +   VR I+ C L + ++   
Sbjct: 120  HHRYSYQVYPPLHVAAMQEAAGYFVGTHDFRGFCATGSPVKDFVRTIWHCTLTVTEENLL 179

Query: 3398 LGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAP 3577
            L          +V G GFL  MVR++ GTL ++G GK+    +   + S    +    AP
Sbjct: 180  L---------MDVMGDGFLYNMVRIITGTLVDVGKGKIAPESIPQIIASRDRTQAGTTAP 230

Query: 3578 SNGLYLCEV 3604
              GL L EV
Sbjct: 231  PQGLALLEV 239



>gi|40062661|gb|AAR37582.1|   tRNA pseudouridine synthase A [uncultured bacterium 313]
          Length = 245

 Score =  121 bits (304), Expect = 5e-26
 Identities = 80/254 (31%), Positives = 128/254 (50%), Gaps = 1/254 (0%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQV 3031
            YKI + Y GT + GWQ Q +  Q+IQ  L+ A+   SK   + T G+GRTDSGVHAL QV
Sbjct: 4    YKIKIEYDGTPFVGWQFQKN-GQSIQEVLQNAIFNFSKEKVVVT-GAGRTDSGVHALAQV 61

Query: 3032 VRVQIPLELEPLSLLKALNSHLPND-IECIHSENSSELFNPVFDAKDKTYKYLFSLNGRR 3208
                +  +++  S L  +N H+ N  +  +    +S+ F+  FDAK +TY+Y        
Sbjct: 62   AHFDLKKKIKKKSFLPGINQHIGNKPVTVLKINKTSKKFHARFDAKKRTYQYTIINRQSP 121

Query: 3209 NALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQ 3388
              L  +    + + +D+  M++  +L +G HDF+ F        S ++ + +  +   K 
Sbjct: 122  LTLQKNKAWHIRKKLDVRAMKKGAKLLLGTHDFSTFRASSCGAKSPIKTMENISIKKNKD 181

Query: 3389 QGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAA 3568
            +  L  +             FL+Q VR MVG +  +G GK +L D K +  S    + A 
Sbjct: 182  KITLKFI----------SRSFLQQQVRSMVGCIKYLGDGKWKLEDFKKSFKSKCRLECAP 231

Query: 3569 VAPSNGLYLCEVNY 3610
             AP++GLYL ++ Y
Sbjct: 232  PAPASGLYLAKIKY 245



>gi|15605190|ref|NP_219976.1|   Pseudouridylate Synthase I [Chlamydia trachomatis]
 gi|8134751|sp|O84469|TRUA_CHLTR   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|7437074|pir||C71511   probable pseudouridylate synthase I - Chlamydia trachomatis
            (serotype D, strain UW3/Cx)
 gi|3328897|gb|AAC68063.1|   Pseudouridylate Synthase I [Chlamydia trachomatis]
          Length = 267

 Score =  121 bits (303), Expect = 6e-26
 Identities = 98/263 (37%), Positives = 135/263 (51%), Gaps = 8/263 (3%)
 Frame = +2

Query: 2855 KIILR--YKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQ 3028
            KI+L+  Y+GT Y GWQ QP+ + +IQ  LE  LKKI+    I  I SGRTD+GVHA GQ
Sbjct: 4    KIVLQIAYQGTSYSGWQYQPN-ALSIQEVLETILKKIA-GFRISVISSGRTDAGVHAQGQ 61

Query: 3029 VVRVQIPLELEPLS---LLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLN 3199
            +     P          + K LN+ LP+DI    +  + E F+  F A  K Y+Y  SL 
Sbjct: 62   IAHFHCPDHPHFTDPRQIQKMLNALLPHDIVIRDAVMTDEDFHSRFSAIAKEYRYTLSLL 121

Query: 3200 GRRNALVDDSMTCLDR--PMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKL 3373
             +   L    + C      ++I +M+EA +  +G HDFA F  +G + SST+R +Y   L
Sbjct: 122  PK--PLPHHRLFCFSPRYKLNIARMQEAAQYLVGTHDFASFANLGREYSSTIRTLY--TL 177

Query: 3374 HLEKQQGFLGEVYPEHYIFEV-KGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPS 3550
             L +Q         EH +  + +G+GFL +MVR +VG L +IG GK     L   L +  
Sbjct: 178  DLSEQ---------EHLVTVICRGNGFLYKMVRNIVGALLDIGKGKYPPEHLLDMLATKD 228

Query: 3551 GAKLAAVAPSNGLYLCEVNY*MP 3619
              K    AP  GL L  V Y  P
Sbjct: 229  RRKGPPSAPPYGLSLHHVCYPPP 251



>gi|30248700|ref|NP_840770.1|   tRNA pseudouridine synthase [Nitrosomonas europaea ATCC 19718]
 gi|30180295|emb|CAD84602.1|   tRNA pseudouridine synthase [Nitrosomonas europaea ATCC 19718]
          Length = 272

 Score =  120 bits (300), Expect = 1e-25
 Identities = 81/256 (31%), Positives = 131/256 (51%), Gaps = 2/256 (0%)
 Frame = +2

Query: 2849 FYKIIL--RYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHAL 3022
            F KI+L   Y G  Y GWQKQP    ++Q +LE AL  ++   +I  + +GRTD+GVHAL
Sbjct: 11   FVKIVLALEYDGRGYCGWQKQPGCL-SVQSRLESALSGVA-GRQIQVVAAGRTDAGVHAL 68

Query: 3023 GQVVRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNG 3202
             QVV ++  +     + ++  N+ LP DI  + +   S+ F+  F A ++TY Y      
Sbjct: 69   CQVVHLETCVRRPLNAWIRGTNALLPGDISILEASEVSDDFHARFSATERTYLYYLLSRP 128

Query: 3203 RRNALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLE 3382
             R  +    +  +  P+D+EKM+ A +L IG+HDF+ F +      + +R +   +L++ 
Sbjct: 129  ARPGIHHGKIGWVHYPLDLEKMQMAAKLLIGKHDFSAFRSSECQSRTAIRQL--TRLNIS 186

Query: 3383 KQQGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKL 3562
            + Q        + ++FE   + FL  MVR ++G L  IG GK     +++ L        
Sbjct: 187  QHQ--------QLFVFEFCANAFLHHMVRNILGGLVYIGRGKYPPEWMRILLEKRDRTLA 238

Query: 3563 AAVAPSNGLYLCEVNY 3610
            A     +GLYL  V Y
Sbjct: 239  APTFSPDGLYLSGVRY 254



>gi|22125494|ref|NP_668917.1|   pseudouridylate synthase I [Yersinia pestis KIM]
 gi|21958390|gb|AAM85168.1|   pseudouridylate synthase I [Yersinia pestis KIM]
          Length = 293

 Score =  120 bits (300), Expect = 1e-25
 Identities = 76/249 (30%), Positives = 124/249 (49%)
 Frame = +2

Query: 2864 LRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVVRVQ 3043
            + Y G++Y GWQ+Q   + ++Q  LE AL K++ ++ I    +GRTD+GVHA GQVV   
Sbjct: 36   IEYNGSRYFGWQRQQEVA-SVQACLEAALSKVA-NEPIGVFCAGRTDAGVHATGQVVHFV 93

Query: 3044 IPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNALVD 3223
                 +  +    +NSHLP DI     +     F+  F A  + Y+Y+   +  R A++ 
Sbjct: 94   TSAVRKDAAWTMGVNSHLPADIAVRWVKTVDNDFHARFSATARRYRYIIFSHRYRPAILA 153

Query: 3224 DSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGFLG 3403
              +T    P+D EKM  A +  +GE+DF  F  V     +  R +   K+          
Sbjct: 154  QGVTHCYMPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKV---------- 203

Query: 3404 EVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAPSN 3583
              +  + + ++K + F+  MVR +VG+L  IG G  ++  +   L      + AA A ++
Sbjct: 204  TRHGAYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKAD 263

Query: 3584 GLYLCEVNY 3610
            GLYL  V+Y
Sbjct: 264  GLYLVSVDY 272



>gi|16122970|ref|NP_406283.1|   tRNA pseudouridine synthase A [Yersinia pestis]
 gi|25009503|sp|Q8ZD27|TRUA_YERPE   tRNA pseudouridine synthase A (Pseudouridylate synthase I)
            (Pseudouridine synthase I) (Uracil hydrolyase)
 gi|25292041|pir||AF0337   pseudouridylate synthase (EC 4.2.1.70) [imported] - Yersinia pestis
            (strain CO92)
 gi|15980744|emb|CAC93005.1|   tRNA pseudouridine synthase A [Yersinia pestis CO92]
          Length = 264

 Score =  120 bits (300), Expect = 1e-25
 Identities = 76/249 (30%), Positives = 124/249 (49%)
 Frame = +2

Query: 2864 LRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQVVRVQ 3043
            + Y G++Y GWQ+Q   + ++Q  LE AL K++ ++ I    +GRTD+GVHA GQVV   
Sbjct: 7    IEYNGSRYFGWQRQQEVA-SVQACLEAALSKVA-NEPIGVFCAGRTDAGVHATGQVVHFV 64

Query: 3044 IPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNALVD 3223
                 +  +    +NSHLP DI     +     F+  F A  + Y+Y+   +  R A++ 
Sbjct: 65   TSAVRKDAAWTMGVNSHLPADIAVRWVKTVDNDFHARFSATARRYRYIIFSHRYRPAILA 124

Query: 3224 DSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGFLG 3403
              +T    P+D EKM  A +  +GE+DF  F  V     +  R +   K+          
Sbjct: 125  QGVTHCYMPLDAEKMERAAQCLLGENDFTSFRAVQCQSRTPWRNVKHVKV---------- 174

Query: 3404 EVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAPSN 3583
              +  + + ++K + F+  MVR +VG+L  IG G  ++  +   L      + AA A ++
Sbjct: 175  TRHGAYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQDVTWMAELLALKDRTRAAATAKAD 234

Query: 3584 GLYLCEVNY 3610
            GLYL  V+Y
Sbjct: 235  GLYLVSVDY 243



>gi|22965972|ref|ZP_00013570.1|   COG0101: Pseudouridylate synthase [Rhodospirillum rubrum]
          Length = 278

 Score =  119 bits (298), Expect = 2e-25
 Identities = 83/255 (32%), Positives = 129/255 (50%), Gaps = 2/255 (0%)
 Frame = +2

Query: 2852 YKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKI-SKSDEIHTIGSGRTDSGVHALGQ 3028
            Y++ + Y G  Y GWQ+Q +   TIQ  LE+A  ++   +  +H  GSGRTDSGVHALGQ
Sbjct: 4    YRLTVEYDGRGYCGWQRQDN-GPTIQQSLEEAAFRLCGVATRVH--GSGRTDSGVHALGQ 60

Query: 3029 VVRVQIPLELEPLSLLKALNSHL-PNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGR 3205
            V  + +P      +++KALN+HL P  I  I +   +E F+  F A++++Y+Y       
Sbjct: 61   VAHLDLPRAYGAATVMKALNAHLRPQPIAVIDAAEVAEDFHARFSAEERSYRYRILNRIA 120

Query: 3206 RNALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEK 3385
               L    +  + RPM+   M EA ++ +G HDF+ F        S V+ + + +     
Sbjct: 121  PPTLDQGRVWWVARPMEAAIMDEAAQVLVGRHDFSSFRAAECQADSPVKTLSELR----- 175

Query: 3386 QQGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLA 3565
                +  V  E ++F  +   FL   VR MVGTL  +G G+     L+ AL +   +   
Sbjct: 176  ----VTRVGDEIHVF-ARARSFLHHQVRNMVGTLALVGDGRWTADRLRAALEACDRSAAG 230

Query: 3566 AVAPSNGLYLCEVNY 3610
              AP +GLY   V +
Sbjct: 231  PTAPPDGLYFLRVRF 245



>gi|39938715|ref|NP_950481.1|   pseudouridylate synthase [Onion yellows phytoplasma]
 gi|39721824|dbj|BAD04314.1|   pseudouridylate synthase [Onion yellows phytoplasma]
          Length = 243

 Score =  117 bits (294), Expect = 7e-25
 Identities = 90/254 (35%), Positives = 126/254 (49%)
 Frame = +2

Query: 2849 FYKIILRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSDEIHTIGSGRTDSGVHALGQ 3028
            FYK+IL Y GT Y G+QKQP    T+Q   EKALKK++  + I T  + RTD GVH+ GQ
Sbjct: 5    FYKLILSYDGTCYYGYQKQPQKI-TVQQTFEKALKKMTHQN-IPTFAASRTDKGVHSQGQ 62

Query: 3029 VVRVQIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRR 3208
             +  Q    L+P    K LN  LP DI       ++  F+  + AK K Y+Y+FS     
Sbjct: 63   TLHFQTTFFLKPTHFQKTLNYLLPPDIRVRQMNFATPNFHARYSAKSKIYQYVFS-KKPL 121

Query: 3209 NALVDDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQ 3388
            NA         D+ +  +K+ +A +   G H+F  F T  T   +  + I+         
Sbjct: 122  NAFNHHFQIFADK-LYFDKITKALKFIEGTHNFFAF-TSETQPKNFSKTIF--------- 170

Query: 3389 QGFLGEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAA 3568
            Q FL E     YI    G+GFLK M+R +VG+L  IG  K+ L   +  L   +  K   
Sbjct: 171  QAFLKET-SHKYILVFHGNGFLKYMIRFLVGSLIEIGKNKLSLEQFQAMLLGNTTKKATL 229

Query: 3569 VAPSNGLYLCEVNY 3610
            +APS  L L ++ Y
Sbjct: 230  LAPSKALVLKKIFY 243



>gi|33596565|ref|NP_884208.1|   tRNA pseudouridine synthase A [Bordetella parapertussis]
 gi|33601118|ref|NP_888678.1|   tRNA pseudouridine synthase A [Bordetella bronchiseptica RB50]
 gi|33566334|emb|CAE37247.1|   tRNA pseudouridine synthase A [Bordetella parapertussis]
 gi|33575553|emb|CAE32631.1|   tRNA pseudouridine synthase A [Bordetella bronchiseptica]
          Length = 270

 Score =  117 bits (294), Expect = 7e-25
 Identities = 79/250 (31%), Positives = 125/250 (50%), Gaps = 1/250 (0%)
 Frame = +2

Query: 2864 LRYKGTQYQGWQKQPHTSQTIQGQLEKALKKISKSD-EIHTIGSGRTDSGVHALGQVVRV 3040
            L Y G+ +QGWQ QPH   T+Q Q+E AL   +     + T+ +GRTD+GVHA  QV+ +
Sbjct: 8    LAYDGSAWQGWQTQPH-GVTVQDQVEAALASFAGGGGPVATVCAGRTDTGVHAAMQVIHL 66

Query: 3041 QIPLELEPLSLLKALNSHLPNDIECIHSENSSELFNPVFDAKDKTYKYLFSLNGRRNALV 3220
               L+    S ++ +N+ LP  I    +   SE F+  F A+ +TY YL      R AL 
Sbjct: 67   DTDLQRRDESWVRGVNAFLPPSIVVQWARPVSEAFHARFSARSRTYVYLLWRGRVRPALW 126

Query: 3221 DDSMTCLDRPMDIEKMREACELFIGEHDFADFYTVGTDISSTVRVIYDCKLHLEKQQGFL 3400
                    +P+D+  MR A    +GEHDF+ F +        VR ++  +L ++++  FL
Sbjct: 127  AGRAGWAFQPLDVPAMRAAARTLLGEHDFSSFRSSQCQARHPVRTLH--RLDIDERGAFL 184

Query: 3401 GEVYPEHYIFEVKGSGFLKQMVRLMVGTLWNIGLGKVELADLKMALNSPSGAKLAAVAPS 3580
                    +F ++ + FL  MVR ++G L  +G G+  +A +   L +      A     
Sbjct: 185  --------VFTLRANAFLHHMVRNLIGALLQVGQGRESVAWMDALLRARDRRLGAPTFMP 236

Query: 3581 NGLYLCEVNY 3610
            +GLYL  + Y
Sbjct: 237  DGLYLSAIEY 246






  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Jan 29, 2004 12:33 AM
  Number of letters in database: 530,881,280
  Number of sequences in database:  1,614,176
  
Lambda     K      H
   0.318    0.135    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 164,245,405
Number of Sequences: 1614176
Number of extensions: 3126958
Number of successful extensions: 7039
Number of sequences better than 10.0: 22
Number of HSP's better than 10.0 without gapping: 6594
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 6994
length of database: 530,881,280
effective HSP length: 132
effective length of database: 317,810,048
effective search space used: 180198297216
frameshift window, decay const: 50,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)