BLASTP 2.2.22 [Sep-27-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
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.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.


Reference for composition-based statistics starting in round 2:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= gi|254780295|ref|YP_003064708.1| tRNA pseudouridine synthase A
[Candidatus Liberibacter asiaticus str. psy62]
         (247 letters)

Database: nr 
           14,124,377 sequences; 4,842,793,630 total letters

Searching..................................................done


Results from round 1


>gi|254780295|ref|YP_003064708.1| tRNA pseudouridine synthase A [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254039972|gb|ACT56768.1| tRNA pseudouridine synthase A [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 247

 Score =  512 bits (1319), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 247/247 (100%), Positives = 247/247 (100%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ
Sbjct: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ
Sbjct: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF
Sbjct: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY
Sbjct: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240

Query: 241 FDSVEYS 247
           FDSVEYS
Sbjct: 241 FDSVEYS 247


>gi|315122856|ref|YP_004063345.1| tRNA pseudouridine synthase A [Candidatus Liberibacter solanacearum
           CLso-ZC1]
 gi|313496258|gb|ADR52857.1| tRNA pseudouridine synthase A [Candidatus Liberibacter solanacearum
           CLso-ZC1]
          Length = 247

 Score =  430 bits (1106), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 203/247 (82%), Positives = 222/247 (89%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           MIRYC+IIEY+GSGY GWQRQKNG SIQG IEKAIFLVTGE + V+GAGRTDSGVHALRQ
Sbjct: 1   MIRYCLIIEYDGSGYVGWQRQKNGVSIQGEIEKAIFLVTGESMTVYGAGRTDSGVHALRQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDLVREWVP  LCKALNA+L IS+ ISIL L +VD++FHARFSAIRRSYLYRIITRQ
Sbjct: 61  VAHFDLVREWVPEKLCKALNAHLNISNDISILELCVVDEKFHARFSAIRRSYLYRIITRQ 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APLALEKGRAW  PK LDCE MR+AAQHL+G+HDFTTFRS+ CQA SPIRTID  D+N  
Sbjct: 121 APLALEKGRAWWFPKDLDCEMMRVAAQHLIGKHDFTTFRSVQCQALSPIRTIDRLDINRL 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++IEIRVVARSFLHTQIRSFVGSLKLVGD KWTS DL+KAL+AQDRK CGPL+P EGLY
Sbjct: 181 GDMIEIRVVARSFLHTQIRSFVGSLKLVGDRKWTSDDLQKALKAQDRKACGPLSPSEGLY 240

Query: 241 FDSVEYS 247
           FDSVEYS
Sbjct: 241 FDSVEYS 247


>gi|222084710|ref|YP_002543239.1| tRNA pseudouridine synthase A [Agrobacterium radiobacter K84]
 gi|221722158|gb|ACM25314.1| tRNA pseudouridine synthase A [Agrobacterium radiobacter K84]
          Length = 266

 Score =  333 bits (853), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 157/247 (63%), Positives = 188/247 (76%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY M +EY+G  Y GWQRQ NG S+QG+IE+AI  +TGE   V GAGRTDSGVHA+ Q
Sbjct: 2   MPRYRMTVEYDGIPYVGWQRQNNGPSVQGAIERAILSLTGETASVRGAGRTDSGVHAVGQ 61

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL +EW P  L  ALNA+L+++ D ++ILN+  VD  F ARFSAIRR YLYRII R
Sbjct: 62  VTHADLSKEWKPHTLRNALNAHLRLAGDRVAILNVMEVDASFDARFSAIRRHYLYRIIVR 121

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLALE GRAW + K +D E M  AAQ LVGRHDFTTFRS+HCQA+SP+RT+D  DV  
Sbjct: 122 RAPLALEAGRAWWVAKDMDHEVMHTAAQTLVGRHDFTTFRSVHCQANSPVRTLDRLDVTR 181

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF G+LKL G+GKWT  D+  AL+A+DRK CGP+APP+GL
Sbjct: 182 SGELIEIRATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVRTALEARDRKACGPVAPPDGL 241

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 242 YFMQVDY 248


>gi|86356072|ref|YP_467964.1| tRNA pseudouridine synthase A [Rhizobium etli CFN 42]
 gi|86280174|gb|ABC89237.1| tRNA pseudouridine synthase A protein [Rhizobium etli CFN 42]
          Length = 267

 Score =  332 bits (850), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 154/247 (62%), Positives = 193/247 (78%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY M +EY+G  Y GWQRQ+NG S+QG+IE A+  +TGE V V GAGRTDSGVHA+ Q
Sbjct: 1   MPRYRMTVEYDGGPYVGWQRQENGPSVQGAIEAAVLSLTGETVSVRGAGRTDSGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL +EW P  L  ALNA+L+++ + +SIL+++ V + F ARFSA+RR YLYRI++R
Sbjct: 61  VIHADLSKEWSPYQLQNALNAHLRLAGERVSILDVAAVPEFFDARFSALRRHYLYRIVSR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLALE G+AW +PK+LD E M  AAQ LVGRHDF+TFRS HCQA+SP+RT+D  DV  
Sbjct: 121 RAPLALEAGKAWWVPKTLDDEVMHAAAQRLVGRHDFSTFRSAHCQANSPVRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF G+LKL G+GKWT  D+E AL+A+DRK CGP+APP+GL
Sbjct: 181 SGALIEIRATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVEAALEARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFLQVDY 247


>gi|327191110|gb|EGE58158.1| tRNA-pseudouridine synthase I protein [Rhizobium etli CNPAF512]
          Length = 266

 Score =  331 bits (849), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 154/247 (62%), Positives = 192/247 (77%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY M +EY+G  Y GWQRQ+NG S+QG+IE A+  +TGE V V GAGRTDSGVHA+ Q
Sbjct: 1   MPRYRMTVEYDGGPYVGWQRQENGPSVQGAIEAAVLSLTGETVSVRGAGRTDSGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL +EW P  L  ALNA+L+++ + +SIL++  V + F ARFSA+RR YLYRI++R
Sbjct: 61  VIHADLSKEWSPYQLQNALNAHLRLAGERVSILDVEAVPEFFDARFSALRRHYLYRIVSR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLALE G+AW +PK+LD E M  AAQ LVGRHDF+TFRS HCQA+SP+RT+D  DV  
Sbjct: 121 RAPLALEAGKAWWVPKTLDHEVMHAAAQRLVGRHDFSTFRSAHCQANSPVRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF G+LKL G+GKWT  D+E AL+A+DRK CGP+APP+GL
Sbjct: 181 SGALIEIRATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVEAALEARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFLQVDY 247


>gi|190890088|ref|YP_001976630.1| tRNA-pseudouridine synthase I protein [Rhizobium etli CIAT 652]
 gi|190695367|gb|ACE89452.1| tRNA-pseudouridine synthase I protein [Rhizobium etli CIAT 652]
          Length = 266

 Score =  329 bits (844), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 152/247 (61%), Positives = 192/247 (77%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY M +EY+G  Y GWQRQ+NG S+QG+IE A+  +TGE V V GAGRTDSGVHA+ Q
Sbjct: 1   MPRYRMTVEYDGGPYVGWQRQENGPSVQGAIEAAVLSLTGETVSVRGAGRTDSGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL ++W P  L  A+NA+L+++ + +SIL++  V + F ARFSA+RR YLYRI++R
Sbjct: 61  VIHADLSKQWSPYQLQNAMNAHLRLAGERVSILDVEAVPEFFDARFSALRRHYLYRIVSR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLALE G+AW +PK+LD E M  AAQ LVGRHDF+TFRS HCQA+SP+RT+D  DV  
Sbjct: 121 RAPLALEAGKAWWVPKTLDHEVMHAAAQRLVGRHDFSTFRSAHCQANSPVRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF G+LKL G+GKWT  D+E AL+A+DRK CGP+APP+GL
Sbjct: 181 SGALIEIRATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVEAALEARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFLQVDY 247


>gi|116250203|ref|YP_766041.1| tRNA pseudouridine synthase A [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115254851|emb|CAK05925.1| putative tRNA pseudouridine synthase [Rhizobium leguminosarum bv.
           viciae 3841]
          Length = 272

 Score =  325 bits (833), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 150/247 (60%), Positives = 190/247 (76%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ M +EY+G  Y GWQRQ+NG S+QG+IE A+  +TGE V V GAGRTDSGVHA+ Q
Sbjct: 1   MPRFRMTVEYDGGPYVGWQRQENGPSVQGAIEAAVLSLTGETVSVRGAGRTDSGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL ++W P  L  ALNA+L+I+ + +S+L++    + F ARFSA+RR YLYRI++R
Sbjct: 61  VIHADLSKDWSPYQLQNALNAHLRIAGERVSVLDVEAAPEFFDARFSALRRHYLYRIVSR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLALE G+AW +PK LD E M  AAQ LVGRHDF+TFR+ HCQA+SP+RT+D  DV  
Sbjct: 121 RAPLALEAGKAWWVPKVLDHEVMHAAAQRLVGRHDFSTFRAAHCQANSPVRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF G+LKL G+GKWT  D+E AL+A+DRK CGP+APP+GL
Sbjct: 181 RGELIEIRATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVEAALKARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFMQVDY 247


>gi|15964174|ref|NP_384527.1| tRNA pseudouridine synthase A [Sinorhizobium meliloti 1021]
 gi|307301319|ref|ZP_07581081.1| tRNA pseudouridine synthase A [Sinorhizobium meliloti BL225C]
 gi|30913403|sp|Q92SH4|TRUA_RHIME RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|15073350|emb|CAC41858.1| Probable tRNA pseudouridine synthase A [Sinorhizobium meliloti
           1021]
 gi|306903775|gb|EFN34362.1| tRNA pseudouridine synthase A [Sinorhizobium meliloti BL225C]
          Length = 247

 Score =  325 bits (833), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 155/247 (62%), Positives = 187/247 (75%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+GS Y GWQRQ NG S+QG+IEKA+  +T E V + GAGRTDSGVHA  Q
Sbjct: 1   MPRYRLTVEYDGSDYVGWQRQDNGPSVQGAIEKAVLSLTRETVSIRGAGRTDSGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL REW    L  ALNA+L ++ + +SIL+++     F ARFSAIRR YLYRII+R
Sbjct: 61  VAHLDLTREWKSYTLQNALNAHLALAGERVSILDVAEAPGDFDARFSAIRRHYLYRIISR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++PLALE  RAW +PK LD + M  AAQ LVG HDFTTFRS HCQA+SP+RT+D  DV  
Sbjct: 121 RSPLALEARRAWWVPKPLDHDAMHEAAQRLVGHHDFTTFRSAHCQATSPLRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF GSLKLVG+GKWT  DL+ AL+A+DRK CGP+APP+GL
Sbjct: 181 AGELIEIRATAQSFLHNQIRSFAGSLKLVGEGKWTPDDLQAALEARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFMRVDY 247


>gi|241202830|ref|YP_002973926.1| tRNA pseudouridine synthase A [Rhizobium leguminosarum bv. trifolii
           WSM1325]
 gi|240856720|gb|ACS54387.1| tRNA pseudouridine synthase A [Rhizobium leguminosarum bv. trifolii
           WSM1325]
          Length = 272

 Score =  325 bits (833), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 150/247 (60%), Positives = 190/247 (76%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ M +EY+G  Y GWQRQ+NG S+QG+IE A+  +TGE V+V GAGRTDSGVHA+ Q
Sbjct: 1   MPRFRMTVEYDGGPYVGWQRQENGHSVQGAIEAAVLSLTGETVLVRGAGRTDSGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL +EW P  L  ALNA+L+++ + +SIL +    + F ARFSA+RR YLYRI++R
Sbjct: 61  VIHADLSKEWSPYQLQNALNAHLRLAGERVSILEVEAAPEFFDARFSALRRHYLYRIVSR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLALE G+AW +PK LD E M  AAQ LVG+HDF+TFR+ HCQA+SP+RT+D  DV  
Sbjct: 121 RAPLALEAGKAWWVPKVLDHEVMHAAAQRLVGKHDFSTFRAAHCQANSPVRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF G+LKL G+GKWT  D+E AL+A+DRK CGP+APP+GL
Sbjct: 181 NGELIEIRATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVEAALEARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFMQVDY 247


>gi|307317990|ref|ZP_07597427.1| tRNA pseudouridine synthase A [Sinorhizobium meliloti AK83]
 gi|306896392|gb|EFN27141.1| tRNA pseudouridine synthase A [Sinorhizobium meliloti AK83]
          Length = 247

 Score =  325 bits (832), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 155/247 (62%), Positives = 187/247 (75%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+GS Y GWQRQ NG S+QG+IEKA+  +T E V + GAGRTDSGVHA  Q
Sbjct: 1   MPRYRLTVEYDGSDYVGWQRQDNGPSVQGAIEKAVLSLTRETVSIRGAGRTDSGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL REW    L  ALNA+L ++ + +SIL+++     F ARFSAIRR YLYRII+R
Sbjct: 61  VAHLDLTREWKSYTLQNALNAHLALAGERVSILDVAEAPGDFDARFSAIRRHYLYRIISR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++PLALE  RAW +PK LD + M  AAQ LVG HDFTTFRS HCQA+SP+RT+D  DV  
Sbjct: 121 RSPLALEARRAWWVPKPLDHDAMHEAAQRLVGHHDFTTFRSAHCQATSPLRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF GSLKLVG+GKWT  DL+ AL+A+DRK CGP+APP+GL
Sbjct: 181 AGELIEIRATAQSFLHNQIRSFAGSLKLVGEGKWTPDDLQAALKARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFMRVDY 247


>gi|227820646|ref|YP_002824616.1| tRNA pseudouridine synthase A [Sinorhizobium fredii NGR234]
 gi|254764861|sp|C3MF26|TRUA_RHISN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|227339645|gb|ACP23863.1| tRNA pseudouridine synthase A [Sinorhizobium fredii NGR234]
          Length = 247

 Score =  324 bits (830), Expect = 7e-87,   Method: Compositional matrix adjust.
 Identities = 154/247 (62%), Positives = 186/247 (75%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+GS Y GWQRQ+NG S+QG+IEKA+  +TGE V + GAGRTDSGVHA+ Q
Sbjct: 1   MPRYRLTVEYDGSDYVGWQRQENGPSVQGAIEKAVLSLTGETVSIRGAGRTDSGVHAMGQ 60

Query: 61  VAHFDLVREW-VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL REW    +           ++ +SIL+ + V  +F ARFSAIRR YLYRII+R
Sbjct: 61  VAHLDLTREWKTHTLRNALNAHLALAAERVSILDAAEVPPEFDARFSAIRRHYLYRIISR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++PLALE  RAW +PK+LD E M  AAQHLVG HDFTTFRS HCQA+SP+RTID  DV  
Sbjct: 121 RSPLALEARRAWWVPKTLDHEAMHEAAQHLVGHHDFTTFRSAHCQANSPLRTIDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF GSLKLVG+GKWT  DL+ AL+A+DRK CGP+APPEGL
Sbjct: 181 SGELIEIRATAQSFLHNQIRSFAGSLKLVGEGKWTPDDLKTALEARDRKACGPVAPPEGL 240

Query: 240 YFDSVEY 246
           +F  V+Y
Sbjct: 241 FFMQVDY 247


>gi|209547671|ref|YP_002279588.1| tRNA pseudouridine synthase A [Rhizobium leguminosarum bv. trifolii
           WSM2304]
 gi|238057734|sp|B5ZN21|TRUA_RHILW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|209533427|gb|ACI53362.1| tRNA pseudouridine synthase A [Rhizobium leguminosarum bv. trifolii
           WSM2304]
          Length = 268

 Score =  324 bits (830), Expect = 8e-87,   Method: Compositional matrix adjust.
 Identities = 150/247 (60%), Positives = 190/247 (76%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ M +EY+G  Y GWQRQ+NG S+QG+IE A+  +TGE V + GAGRTDSGVHA+ Q
Sbjct: 1   MPRFRMTVEYDGGPYVGWQRQENGPSVQGAIEAAVLSLTGETVSIRGAGRTDSGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL + W P  L  ALNA+L+++ + +SIL++  V + F ARFSA+RR YLYRI++R
Sbjct: 61  VIHADLSKAWSPYQLQNALNAHLRLAGERVSILDVEAVAEFFDARFSALRRHYLYRIVSR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLALE G+AW +PK LD E M  AAQ LVGRHDF+TFR+ HCQA+SP+RT+D  DV  
Sbjct: 121 RAPLALEAGKAWWVPKVLDHEVMHAAAQRLVGRHDFSTFRAAHCQANSPVRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G LIEIR  A+SFLH QIRSF G+LKL G+GKWT  D+E AL+A+DRK CGP+APP+GL
Sbjct: 181 SGELIEIRATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVEAALEARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFLQVDY 247


>gi|150395284|ref|YP_001325751.1| tRNA pseudouridine synthase A [Sinorhizobium medicae WSM419]
 gi|166229839|sp|A6U5I6|TRUA_SINMW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|150026799|gb|ABR58916.1| tRNA pseudouridine synthase A [Sinorhizobium medicae WSM419]
          Length = 247

 Score =  320 bits (821), Expect = 8e-86,   Method: Compositional matrix adjust.
 Identities = 152/247 (61%), Positives = 188/247 (76%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +I+EY+G+ Y GWQRQ NG S+QG+IEKA+  +TGE V V GAGRTDSGVHA  Q
Sbjct: 1   MPRFRLIVEYDGTDYVGWQRQDNGPSVQGAIEKAVLSLTGETVRVRGAGRTDSGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL R W P  L  ALNA+L ++ + +SIL +      F ARFSAIRR YLYRII+R
Sbjct: 61  VAHLDLTRAWKPYTLQNALNAHLSLAGERVSILEVEEAAADFDARFSAIRRHYLYRIISR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++PLALE  RAW +PK+LD + M  AAQ L+G HDFTTFRS +CQA+SP+RT+D  DV  
Sbjct: 121 RSPLALEARRAWWVPKALDHDAMHEAAQRLLGHHDFTTFRSANCQATSPMRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LIEIR  A+SFLH QIRSF GSLKLVG+ KWT  +L+ AL+A+DRK CGP+APP+GL
Sbjct: 181 TGDLIEIRASAQSFLHNQIRSFAGSLKLVGESKWTPDNLQAALEARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFMRVDY 247


>gi|325291802|ref|YP_004277666.1| tRNA pseudouridine synthase A [Agrobacterium sp. H13-3]
 gi|325059655|gb|ADY63346.1| tRNA pseudouridine synthase A [Agrobacterium sp. H13-3]
          Length = 266

 Score =  318 bits (814), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 148/247 (59%), Positives = 188/247 (76%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ M +EY+G+ YFGWQRQ NG S+QG++E A+  +TGE V + GAGRTDSGVHA+ Q
Sbjct: 1   MPRFRMTVEYDGTPYFGWQRQDNGPSVQGALEAAVRSLTGETVSIRGAGRTDSGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL R+W P  L  ALNA+L ++ + +S+++++ V + F ARFSA+RR YLYRII R
Sbjct: 61  VAHVDLSRDWAPYKLRNALNAHLAMAKEAVSVIDVTAVTEDFDARFSALRRHYLYRIICR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +A LALE  RAW + K LD E M  AAQ LVGRHDFTTFRS+HCQASSP+RT+D  DV  
Sbjct: 121 KARLALEHKRAWWVSKDLDHERMHEAAQMLVGRHDFTTFRSVHCQASSPVRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LIEIR  A+SFLH QIRSF G+LK+ G+G  T  D+  AL+A+DRK CGP+APP+GL
Sbjct: 181 NGDLIEIRATAQSFLHNQIRSFAGTLKMAGEGSMTPEDVRAALEARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFMQVDY 247


>gi|218508236|ref|ZP_03506114.1| tRNA pseudouridine synthase A [Rhizobium etli Brasil 5]
          Length = 238

 Score =  317 bits (811), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 185/238 (77%), Gaps = 1/238 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G  Y GWQRQ+NG S+QG+IE A+  +TGE V V GAGRTDSGVHA+ Q
Sbjct: 1   MPRYRITVEYDGGPYVGWQRQENGPSVQGAIEAAVLSLTGETVSVRGAGRTDSGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL +EW P  L  ALNA+L+++ + +SIL++  V + F ARFSA+RR YLYRI++R
Sbjct: 61  VIHADLSKEWSPYQLQNALNAHLRLAGERVSILDVEAVPEFFDARFSALRRHYLYRIVSR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLALE G+AW +PK+LD E M  AAQ LVGRHDF+TFRS HCQA+SP+RT+D  DV  
Sbjct: 121 RAPLALEAGKAWWVPKTLDHEVMHAAAQRLVGRHDFSTFRSAHCQANSPVRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            G LIEIR  A+SFLH QIRSF G+LKL G+GKWT  D+E AL+A+DRK CGP+APP+
Sbjct: 181 SGALIEIRATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVEAALEARDRKACGPVAPPD 238


>gi|222147430|ref|YP_002548387.1| tRNA pseudouridine synthase A [Agrobacterium vitis S4]
 gi|254789600|sp|B9JQX0|TRUA_AGRVS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|221734420|gb|ACM35383.1| tRNA pseudouridine synthase A [Agrobacterium vitis S4]
          Length = 259

 Score =  308 bits (790), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 146/247 (59%), Positives = 182/247 (73%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ Y GWQRQ NG S+QG++E A+  +TGE V + GAGRTDSGVHA  Q
Sbjct: 1   MPRYKLTVEYDGTPYVGWQRQDNGPSVQGALEAAVLGLTGETVAIRGAGRTDSGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL+R+W+P  L  ALNA+L +    ISIL    V   F ARFSA++R YLYRI++R
Sbjct: 61  VAHVDLLRQWIPYKLRNALNAHLAQAGQAISILAAEAVPDAFDARFSALKRHYLYRIMSR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            + LALE  RAW + K LD E M  AAQ LVG HDFTTFRS+HCQA SP+RT+D  DV+ 
Sbjct: 121 PSRLALEANRAWWVSKPLDHEAMHAAAQMLVGNHDFTTFRSVHCQAISPVRTLDRLDVSR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LIEIR  A+SFLH QIRSF G+LK+ G+GK T  D+  AL+A+DRK CGP+APP+GL
Sbjct: 181 NGDLIEIRASAQSFLHNQIRSFAGTLKMAGEGKMTPEDVRAALEARDRKACGPVAPPQGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFLQVDY 247


>gi|15887719|ref|NP_353400.1| tRNA pseudouridine synthase A [Agrobacterium tumefaciens str. C58]
 gi|42559844|sp|Q8UIC9|TRUA_AGRT5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|15155280|gb|AAK86185.1| tRNA pseudouridine synthase I [Agrobacterium tumefaciens str. C58]
          Length = 266

 Score =  302 bits (773), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 146/247 (59%), Positives = 188/247 (76%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ M +EY+G+ Y+GWQRQ+NG S+QG++E A+  +TGE V + GAGRTDSGVHA+ Q
Sbjct: 1   MPRFRMTVEYDGTPYYGWQRQENGPSVQGALEAAVRSLTGESVSIRGAGRTDSGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL R+W P  L  ALNA+L ++ + +++L+ + V + F ARFSA+RR YLYRII R
Sbjct: 61  VAHIDLSRDWEPYKLRNALNAHLAMAGEAVAVLDAAAVTEDFDARFSALRRHYLYRIICR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++ LALE  RAW + K LD E M  AAQ LVGRHDFTTFRS+HCQA+SP+RT+D  DV  
Sbjct: 121 KSRLALEHKRAWWVSKDLDHERMHEAAQMLVGRHDFTTFRSVHCQANSPVRTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LIEIR  A+SFLH QIRSF G+LKL G+G  T  D+  AL+A+DRK CGP+APP+GL
Sbjct: 181 NGDLIEIRATAQSFLHNQIRSFAGTLKLAGEGGMTPDDVRAALEARDRKACGPVAPPDGL 240

Query: 240 YFDSVEY 246
           YF  V+Y
Sbjct: 241 YFMQVDY 247


>gi|182677494|ref|YP_001831640.1| tRNA pseudouridine synthase A [Beijerinckia indica subsp. indica
           ATCC 9039]
 gi|238691224|sp|B2IEW0|TRUA_BEII9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|182633377|gb|ACB94151.1| tRNA pseudouridine synthase A [Beijerinckia indica subsp. indica
           ATCC 9039]
          Length = 260

 Score =  290 bits (742), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 137/246 (55%), Positives = 176/246 (71%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ + GWQRQKNG S+Q  IE A+  + G  V + GAGRTD+GVHA  Q
Sbjct: 1   MPRYKLTVEYDGASFVGWQRQKNGLSVQEVIETALLAINGAPVGIRGAGRTDAGVHASAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL REW P +L  ALNA+++ +  ++++    V + F ARFSAIRR YLYRII R+
Sbjct: 61  VAHADLAREWRPDVLRDALNAHMRPA-LVAVVAAEPVPETFDARFSAIRRHYLYRIINRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL  E GRAWL+ + LD   M  AAQ L GRHDF+TFR+  CQA+SPIRT++  DV + 
Sbjct: 120 APLTFEAGRAWLVKRRLDARAMHEAAQVLTGRHDFSTFRAAECQAASPIRTLERLDVQAV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LIEIR  ARSFLH Q+RS VGSL++VG GKW++ DL  AL+A DR+ CG +AP  GLY
Sbjct: 180 GDLIEIRASARSFLHHQVRSMVGSLEMVGSGKWSAGDLRAALEACDRRRCGMVAPAAGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LTGVDY 245


>gi|163757847|ref|ZP_02164936.1| tRNA pseudouridine synthase A [Hoeflea phototrophica DFL-43]
 gi|162285349|gb|EDQ35631.1| tRNA pseudouridine synthase A [Hoeflea phototrophica DFL-43]
          Length = 255

 Score =  283 bits (723), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 141/250 (56%), Positives = 177/250 (70%), Gaps = 3/250 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+GSGY GWQRQ +  SIQ +IE AI    G+ V + GAGRTD+GVHA  Q
Sbjct: 1   MPRYRLDIEYDGSGYAGWQRQDDHPSIQQAIETAIHGFCGQAVSIRGAGRTDAGVHAWGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL  +W    +  A+NA+L+++ + ++IL    V + F ARFSA RR Y+YRII R
Sbjct: 61  VAHVDLENQWSDDTVRDAINAHLQMARERVAILAAREVPEDFDARFSATRRHYVYRIICR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN- 178
           +APL +EK RA   P+ LD E M  AAQ LVGRHDFTTFRS+ CQA SP+R++D  DV  
Sbjct: 121 RAPLVIEKNRALWSPRPLDAEAMHEAAQRLVGRHDFTTFRSVQCQADSPVRSLDRLDVTR 180

Query: 179 -SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
             F  LIEI   ARSFLH QIRSF G+L+LVG+GKWT+ D++ AL+A+ RK CGP+A PE
Sbjct: 181 GGFDGLIEIHATARSFLHNQIRSFAGTLRLVGEGKWTADDVQIALEARSRKACGPVAAPE 240

Query: 238 GLYFDSVEYS 247
           GLYF  V+Y 
Sbjct: 241 GLYFRQVDYD 250


>gi|218658453|ref|ZP_03514383.1| tRNA pseudouridine synthase A [Rhizobium etli IE4771]
          Length = 244

 Score =  280 bits (717), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 132/213 (61%), Positives = 166/213 (77%), Gaps = 1/213 (0%)

Query: 35  IFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS-DTISILN 93
           +  +TGE V V GAGRTDSGVHA+ QV H DL +EW P  L  ALNA+L+++ + +SIL+
Sbjct: 13  VLSLTGETVSVRGAGRTDSGVHAMGQVIHVDLSKEWSPYQLQNALNAHLRLAGERVSILD 72

Query: 94  LSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRH 153
           +  V + F ARFSA+RR YLYRI++R+APLALE G+AW +PK+LD E M  AAQ LVGRH
Sbjct: 73  VEAVPEFFDARFSALRRHYLYRIVSRRAPLALEAGKAWWVPKTLDHEVMHAAAQRLVGRH 132

Query: 154 DFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW 213
           DF+TFRS HCQA+SP+RT+D  DV   G LIEIR  A+SFLH QIRSF G+LKL G+GKW
Sbjct: 133 DFSTFRSAHCQANSPVRTLDRLDVTRSGALIEIRATAQSFLHNQIRSFAGTLKLAGEGKW 192

Query: 214 TSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           T  D+E AL+A++RK CGP+APP+GLYF  V+Y
Sbjct: 193 TPDDVEAALEARNRKACGPVAPPDGLYFLQVDY 225


>gi|217977314|ref|YP_002361461.1| tRNA pseudouridine synthase A [Methylocella silvestris BL2]
 gi|254789643|sp|B8ENG8|TRUA_METSB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|217502690|gb|ACK50099.1| tRNA pseudouridine synthase A [Methylocella silvestris BL2]
          Length = 248

 Score =  280 bits (716), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 138/246 (56%), Positives = 173/246 (70%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ ++IEY+G+ + GWQRQ NG S+Q +IE A+   TGE V +HGAGRTD+GVHA  Q
Sbjct: 1   MPRFKLLIEYDGAPFVGWQRQANGFSVQEAIETALGGFTGESVAIHGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D  R+W P +L  A NA+L+  + I+IL    VD +F ARFSA+RR YLY+II R+
Sbjct: 61  VAHVDFSRDWRPDVLRDAANAWLR-PNPIAILKAERVDDEFSARFSAVRRHYLYKIINRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A L LE GR W I +SLD   M  AAQ L+G HDF+TFR   CQA SP+RT++ FDV   
Sbjct: 120 ASLTLEAGRCWAIRRSLDAGAMHEAAQTLLGFHDFSTFRDSECQAESPLRTLERFDVLRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  IEI V ARSFLH+Q+RS VGSL  VG GKW   D+ +AL A+DR+ CG +APPEGLY
Sbjct: 180 GENIEIHVAARSFLHSQVRSMVGSLAHVGSGKWRVEDMAEALAAKDRRRCGVVAPPEGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LMQVDY 245


>gi|163867374|ref|YP_001608568.1| tRNA pseudouridine synthase A [Bartonella tribocorum CIP 105476]
 gi|189029992|sp|A9ILJ7|TRUA_BART1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|161017015|emb|CAK00573.1| tRNA pseudouridine synthase A [Bartonella tribocorum CIP 105476]
          Length = 247

 Score =  278 bits (712), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 136/247 (55%), Positives = 171/247 (69%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+GS Y GWQRQ    +IQG++E+AIF  +G+ + +  AGRTD+GVHA  Q
Sbjct: 1   MSRFKLTLEYDGSNYAGWQRQAKLHTIQGALEQAIFRFSGQQLTITTAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKI-SDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D ++ W P  +  ALNA L+  S+ ISILN+  V   F ARFSAI+R YL++I+ R
Sbjct: 61  VAHVDFIKNWPPHTVRDALNALLRQQSEAISILNVENVPDDFDARFSAIKRHYLFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++P AL   R W IPK L+ + M  AAQ LVG+HDFTTFRS HCQA SPIRT++  D+  
Sbjct: 121 RSPPALNAKRVWWIPKPLNAQAMHEAAQKLVGQHDFTTFRSAHCQAKSPIRTLERLDIQK 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I I   ARSFLH QIRSF GSL  VG G+WT+ DLE AL A+DRK CG +APP GL
Sbjct: 181 EGEEIFIYAKARSFLHHQIRSFAGSLMEVGIGRWTAQDLEAALHAKDRKRCGVVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   VEY
Sbjct: 241 YLTKVEY 247


>gi|17988610|ref|NP_541243.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 1 str. 16M]
 gi|62317861|ref|YP_223714.1| tRNA pseudouridine synthase A [Brucella abortus bv. 1 str. 9-941]
 gi|83269839|ref|YP_419130.1| tRNA pseudouridine synthase A [Brucella melitensis biovar Abortus
           2308]
 gi|148558621|ref|YP_001257944.1| tRNA pseudouridine synthase A [Brucella ovis ATCC 25840]
 gi|161621080|ref|YP_001594966.1| tRNA pseudouridine synthase A [Brucella canis ATCC 23365]
 gi|163845146|ref|YP_001622801.1| tRNA pseudouridine synthase A [Brucella suis ATCC 23445]
 gi|221090245|ref|YP_002519393.1| tRNA pseudouridine synthase A [Brucella suis 1330]
 gi|225629482|ref|ZP_03787515.1| tRNA pseudouridine synthase A [Brucella ceti str. Cudo]
 gi|225686787|ref|YP_002734759.1| tRNA pseudouridine synthase A [Brucella melitensis ATCC 23457]
 gi|237817402|ref|ZP_04596394.1| tRNA pseudouridine synthase A [Brucella abortus str. 2308 A]
 gi|254690653|ref|ZP_05153907.1| tRNA pseudouridine synthase A [Brucella abortus bv. 6 str. 870]
 gi|254696042|ref|ZP_05157870.1| tRNA pseudouridine synthase A [Brucella abortus bv. 3 str. Tulya]
 gi|254699151|ref|ZP_05160979.1| tRNA pseudouridine synthase A [Brucella abortus bv. 2 str. 86/8/59]
 gi|254700227|ref|ZP_05162055.1| tRNA pseudouridine synthase A [Brucella suis bv. 5 str. 513]
 gi|254703348|ref|ZP_05165176.1| tRNA pseudouridine synthase A [Brucella suis bv. 3 str. 686]
 gi|254705511|ref|ZP_05167339.1| tRNA pseudouridine synthase A [Brucella pinnipedialis M163/99/10]
 gi|254710742|ref|ZP_05172553.1| tRNA pseudouridine synthase A [Brucella pinnipedialis B2/94]
 gi|254712788|ref|ZP_05174599.1| tRNA pseudouridine synthase A [Brucella ceti M644/93/1]
 gi|254715857|ref|ZP_05177668.1| tRNA pseudouridine synthase A [Brucella ceti M13/05/1]
 gi|254732595|ref|ZP_05191173.1| tRNA pseudouridine synthase A [Brucella abortus bv. 4 str. 292]
 gi|256015792|ref|YP_003105801.1| tRNA pseudouridine synthase A [Brucella microti CCM 4915]
 gi|256029125|ref|ZP_05442739.1| tRNA pseudouridine synthase A [Brucella pinnipedialis M292/94/1]
 gi|256043901|ref|ZP_05446820.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256058808|ref|ZP_05449024.1| tRNA pseudouridine synthase A [Brucella neotomae 5K33]
 gi|256111035|ref|ZP_05452097.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 3 str.
           Ether]
 gi|256157317|ref|ZP_05455235.1| tRNA pseudouridine synthase A [Brucella ceti M490/95/1]
 gi|256253705|ref|ZP_05459241.1| tRNA pseudouridine synthase A [Brucella ceti B1/94]
 gi|256255835|ref|ZP_05461371.1| tRNA pseudouridine synthase A [Brucella abortus bv. 9 str. C68]
 gi|256262079|ref|ZP_05464611.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 2 str. 63/9]
 gi|260167783|ref|ZP_05754594.1| tRNA pseudouridine synthase A [Brucella sp. F5/99]
 gi|260545096|ref|ZP_05820917.1| tRNA pseudouridine synthase A [Brucella abortus NCTC 8038]
 gi|260565077|ref|ZP_05835562.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 1 str. 16M]
 gi|260567722|ref|ZP_05838191.1| tRNA pseudouridine synthase A [Brucella suis bv. 4 str. 40]
 gi|260756224|ref|ZP_05868572.1| pseudouridylate synthase [Brucella abortus bv. 6 str. 870]
 gi|260760407|ref|ZP_05872755.1| pseudouridylate synthase [Brucella abortus bv. 4 str. 292]
 gi|260763647|ref|ZP_05875979.1| pseudouridylate synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260882048|ref|ZP_05893662.1| tRNA pseudouridine synthase A [Brucella abortus bv. 9 str. C68]
 gi|261216474|ref|ZP_05930755.1| pseudouridylate synthase [Brucella abortus bv. 3 str. Tulya]
 gi|261217618|ref|ZP_05931899.1| tRNA pseudouridine synthase A [Brucella ceti M13/05/1]
 gi|261220842|ref|ZP_05935123.1| tRNA pseudouridine synthase A [Brucella ceti B1/94]
 gi|261312915|ref|ZP_05952112.1| tRNA pseudouridine synthase A [Brucella pinnipedialis M163/99/10]
 gi|261318310|ref|ZP_05957507.1| tRNA pseudouridine synthase A [Brucella pinnipedialis B2/94]
 gi|261320495|ref|ZP_05959692.1| tRNA pseudouridine synthase A [Brucella ceti M644/93/1]
 gi|261322745|ref|ZP_05961942.1| tRNA pseudouridine synthase A [Brucella neotomae 5K33]
 gi|261750722|ref|ZP_05994431.1| tRNA pseudouridine synthase A [Brucella suis bv. 5 str. 513]
 gi|261753978|ref|ZP_05997687.1| tRNA pseudouridine synthase A [Brucella suis bv. 3 str. 686]
 gi|261757220|ref|ZP_06000929.1| tRNA pseudouridine synthase A [Brucella sp. F5/99]
 gi|265986108|ref|ZP_06098665.1| tRNA pseudouridine synthase A [Brucella pinnipedialis M292/94/1]
 gi|265990323|ref|ZP_06102880.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265992570|ref|ZP_06105127.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 3 str.
           Ether]
 gi|265995802|ref|ZP_06108359.1| tRNA pseudouridine synthase A [Brucella ceti M490/95/1]
 gi|294853986|ref|ZP_06794658.1| tRNA pseudouridine synthase A [Brucella sp. NVSL 07-0026]
 gi|297249204|ref|ZP_06932905.1| tRNA pseudouridine synthase A [Brucella abortus bv. 5 str. B3196]
 gi|30913400|sp|Q8YDB2|TRUA_BRUME RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901254|sp|Q60CV4|TRUA_BRUSU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|81309258|sp|Q576T1|TRUA_BRUAB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123754475|sp|Q2YJQ4|TRUA_BRUA2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228682|sp|A5VVT9|TRUA_BRUO2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030128|sp|A9MCV8|TRUA_BRUC2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030129|sp|A9WW43|TRUA_BRUSI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254789607|sp|C0RMH2|TRUA_BRUMB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|17984412|gb|AAL53507.1| tRNA pseudouridine synthase a [Brucella melitensis bv. 1 str. 16M]
 gi|54112373|gb|AAV28867.1| tRNA pseudouridine synthase A [Brucella suis 1330]
 gi|62198054|gb|AAX76353.1| TruA, tRNA pseudouridine synthase A [Brucella abortus bv. 1 str.
           9-941]
 gi|82940113|emb|CAJ13161.1| tRNA pseudouridine synthase [Brucella melitensis biovar Abortus
           2308]
 gi|148369906|gb|ABQ62778.1| tRNA pseudouridine synthase A [Brucella ovis ATCC 25840]
 gi|161337891|gb|ABX64195.1| tRNA pseudouridine synthase A [Brucella canis ATCC 23365]
 gi|163675869|gb|ABY39979.1| tRNA pseudouridine synthase A [Brucella suis ATCC 23445]
 gi|225615978|gb|EEH13027.1| tRNA pseudouridine synthase A [Brucella ceti str. Cudo]
 gi|225642892|gb|ACO02805.1| tRNA pseudouridine synthase A [Brucella melitensis ATCC 23457]
 gi|237788215|gb|EEP62431.1| tRNA pseudouridine synthase A [Brucella abortus str. 2308 A]
 gi|255998452|gb|ACU50139.1| tRNA pseudouridine synthase A [Brucella microti CCM 4915]
 gi|260098367|gb|EEW82241.1| tRNA pseudouridine synthase A [Brucella abortus NCTC 8038]
 gi|260152720|gb|EEW87813.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 1 str. 16M]
 gi|260154387|gb|EEW89468.1| tRNA pseudouridine synthase A [Brucella suis bv. 4 str. 40]
 gi|260670725|gb|EEX57665.1| pseudouridylate synthase [Brucella abortus bv. 4 str. 292]
 gi|260674068|gb|EEX60889.1| pseudouridylate synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260676332|gb|EEX63153.1| pseudouridylate synthase [Brucella abortus bv. 6 str. 870]
 gi|260871576|gb|EEX78645.1| tRNA pseudouridine synthase A [Brucella abortus bv. 9 str. C68]
 gi|260918081|gb|EEX84942.1| pseudouridylate synthase [Brucella abortus bv. 3 str. Tulya]
 gi|260919426|gb|EEX86079.1| tRNA pseudouridine synthase A [Brucella ceti B1/94]
 gi|260922707|gb|EEX89275.1| tRNA pseudouridine synthase A [Brucella ceti M13/05/1]
 gi|261293185|gb|EEX96681.1| tRNA pseudouridine synthase A [Brucella ceti M644/93/1]
 gi|261297533|gb|EEY01030.1| tRNA pseudouridine synthase A [Brucella pinnipedialis B2/94]
 gi|261298725|gb|EEY02222.1| tRNA pseudouridine synthase A [Brucella neotomae 5K33]
 gi|261301941|gb|EEY05438.1| tRNA pseudouridine synthase A [Brucella pinnipedialis M163/99/10]
 gi|261737204|gb|EEY25200.1| tRNA pseudouridine synthase A [Brucella sp. F5/99]
 gi|261740475|gb|EEY28401.1| tRNA pseudouridine synthase A [Brucella suis bv. 5 str. 513]
 gi|261743731|gb|EEY31657.1| tRNA pseudouridine synthase A [Brucella suis bv. 3 str. 686]
 gi|262550099|gb|EEZ06260.1| tRNA pseudouridine synthase A [Brucella ceti M490/95/1]
 gi|262763440|gb|EEZ09472.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 3 str.
           Ether]
 gi|263000992|gb|EEZ13682.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263091768|gb|EEZ16099.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 2 str. 63/9]
 gi|264658305|gb|EEZ28566.1| tRNA pseudouridine synthase A [Brucella pinnipedialis M292/94/1]
 gi|294819641|gb|EFG36641.1| tRNA pseudouridine synthase A [Brucella sp. NVSL 07-0026]
 gi|297173073|gb|EFH32437.1| tRNA pseudouridine synthase A [Brucella abortus bv. 5 str. B3196]
 gi|326411195|gb|ADZ68259.1| tRNA pseudouridine synthase A [Brucella melitensis M28]
 gi|326554486|gb|ADZ89125.1| tRNA pseudouridine synthase A [Brucella melitensis M5-90]
          Length = 251

 Score =  278 bits (711), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 132/248 (53%), Positives = 175/248 (70%), Gaps = 1/248 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ Y GWQRQ+NG ++QG+IE+A     GE + +  AGRTD+GVHA  Q
Sbjct: 1   MPRYKLTVEYDGTPYVGWQRQENGHAVQGAIEQAFKKFCGEDLTLSAAGRTDAGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL ++W    +  A+NA+L ++D  ISILN+      F ARFSA  R YLYRI  R
Sbjct: 61  VAHVDLAKDWGAGKVRDAVNAHLVMADERISILNVEKTTDTFDARFSARARHYLYRIHNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLA++  RAW + K LD + M  AAQ L+G HDFTTFR+  CQA SP++T+D  DV  
Sbjct: 121 RAPLAVDYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQCQAKSPVKTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+++E+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+A+DRK CG +APP GL
Sbjct: 181 NGDMVEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALEARDRKACGQVAPPYGL 240

Query: 240 YFDSVEYS 247
           Y   V+Y+
Sbjct: 241 YLVGVDYA 248


>gi|110632752|ref|YP_672960.1| tRNA pseudouridine synthase A [Mesorhizobium sp. BNC1]
 gi|123162871|sp|Q11LD0|TRUA_MESSB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|110283736|gb|ABG61795.1| tRNA pseudouridine synthase A [Chelativorans sp. BNC1]
          Length = 247

 Score =  277 bits (709), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 140/247 (56%), Positives = 175/247 (70%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IEY+G  Y GWQRQ    S+Q +IEKAI   +GE V + GAGRTD+GVHAL Q
Sbjct: 1   MHRFRIDIEYDGGPYAGWQRQAGQHSVQEAIEKAIAAFSGEEVTIRGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAHFDL REW    +  ALNA+L ++ + +SIL    V + F ARFSA  R YLYRI  R
Sbjct: 61  VAHFDLSREWKSDKVRDALNAHLTLAGEAVSILRAEAVAEDFDARFSAKARHYLYRIANR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++PLALE+GRAW + + LD   M  AAQ LVG+HDFTTFRS+ CQA SP++T+D  DV  
Sbjct: 121 RSPLALERGRAWHVARRLDAAAMHEAAQRLVGKHDFTTFRSVQCQAKSPVKTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ IEI   ARSFLH Q+RS VG+LK VG+G WT+ D + ALQA+DR  CGP+APP+GL
Sbjct: 181 VGDEIEIHASARSFLHNQVRSLVGTLKKVGEGGWTADDAQAALQARDRAACGPVAPPQGL 240

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLVRVDY 247


>gi|254720140|ref|ZP_05181951.1| tRNA pseudouridine synthase A [Brucella sp. 83/13]
 gi|265985146|ref|ZP_06097881.1| tRNA pseudouridine synthase A [Brucella sp. 83/13]
 gi|264663738|gb|EEZ33999.1| tRNA pseudouridine synthase A [Brucella sp. 83/13]
          Length = 251

 Score =  277 bits (708), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 132/248 (53%), Positives = 174/248 (70%), Gaps = 1/248 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ Y GWQRQ+NG ++QG+IE+A     GE + +  AGRTD+GVHA  Q
Sbjct: 1   MPRYKLTVEYDGTPYVGWQRQENGHAVQGAIEQAFKKFCGEELTLSAAGRTDAGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL ++W    +  A+NA+L ++D  ISILN+      F ARFSA  R YLYRI  R
Sbjct: 61  VAHVDLAKDWGAGKVRDAVNAHLVMADERISILNVEKTTDTFDARFSARARHYLYRIHNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLA+   RAW + K LD + M  AAQ L+G HDFTTFR+  CQA SP++T+D  DV  
Sbjct: 121 RAPLAVNYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQCQAKSPVKTLDRLDVTR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+++E+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+A+DRK CG +APP GL
Sbjct: 181 NGDMVEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALEARDRKACGQVAPPYGL 240

Query: 240 YFDSVEYS 247
           Y   V+Y+
Sbjct: 241 YLVGVDYA 248


>gi|56551706|ref|YP_162545.1| tRNA pseudouridine synthase A [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241762299|ref|ZP_04760380.1| tRNA pseudouridine synthase A [Zymomonas mobilis subsp. mobilis
           ATCC 10988]
 gi|260752717|ref|YP_003225610.1| tRNA pseudouridine synthase A [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|59803041|sp|Q9REQ0|TRUA_ZYMMO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56543280|gb|AAV89434.1| tRNA pseudouridine synthase A [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241373202|gb|EER62832.1| tRNA pseudouridine synthase A [Zymomonas mobilis subsp. mobilis
           ATCC 10988]
 gi|258552080|gb|ACV75026.1| tRNA pseudouridine synthase A [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
          Length = 245

 Score =  276 bits (705), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 133/246 (54%), Positives = 171/246 (69%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +E++G  + GWQRQK+G++IQGSIE+A   + G+   V  AGRTD+GVH L  
Sbjct: 1   MNRYRLTVEFDGRNFMGWQRQKHGATIQGSIEEAGASIAGQPTPVQAAGRTDAGVHGLAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AH D+ R++ P  L +ALNA LK    I+IL+   VD ++HARFS I R YLYRII R+
Sbjct: 61  TAHIDVARDFTPFRLMEALNARLK-PRPIAILSCEQVDPEWHARFSCIGRRYLYRIINRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL LE GRAW + K LD E M IAA+ L+G HDFTTFRS+HCQ+ SP++T+DH DV   
Sbjct: 120 PPLTLEAGRAWHVIKPLDAETMDIAAKRLIGLHDFTTFRSVHCQSKSPVKTLDHLDVRRI 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ IEI   ARSFLH Q+RS VG L LVG G+WT+ D+  AL+A++R   G  APP+GLY
Sbjct: 180 GDQIEITAAARSFLHHQVRSMVGCLVLVGQGQWTADDMTTALEARNRAALGFNAPPDGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FTQAIY 245


>gi|240849747|ref|YP_002971135.1| tRNA pseudouridine synthase A [Bartonella grahamii as4aup]
 gi|240266870|gb|ACS50458.1| tRNA pseudouridine synthase A [Bartonella grahamii as4aup]
          Length = 247

 Score =  275 bits (704), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 133/247 (53%), Positives = 169/247 (68%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+GS Y GWQRQ    ++QG++E+AIF  +G+ + +  AGRTD+GVHA  Q
Sbjct: 1   MPRFKLTLEYDGSNYAGWQRQAKLHTVQGALEQAIFSFSGQQLTITTAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D ++ W P  +  ALNA L K  + ISILN+  V   F ARFSA++R Y+++I+ R
Sbjct: 61  VAHVDFIKNWHPHTVRDALNALLRKQGEAISILNVQNVPDDFDARFSAVKRHYIFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++P AL   R W +PK L+ E M  AAQ LVG HDFTTFRS HCQA SPIRT+D  D+  
Sbjct: 121 RSPPALNAKRVWWLPKPLNAEAMHEAAQKLVGEHDFTTFRSAHCQAKSPIRTLDRLDIQR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I +   ARSFLH QIRSF GSL  VG G+WT+ DLE AL A+DRK CG +APP GL
Sbjct: 181 EGEEIFLYAQARSFLHHQIRSFAGSLMEVGIGRWTAQDLEAALHAKDRKHCGVVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   VEY
Sbjct: 241 YLTKVEY 247


>gi|319780351|ref|YP_004139827.1| tRNA pseudouridine synthase A [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317166239|gb|ADV09777.1| tRNA pseudouridine synthase A [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 256

 Score =  275 bits (703), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 132/247 (53%), Positives = 176/247 (71%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IEY+GS + GWQ Q +  S+Q +IE+AI    GE + +  AGRTD+GVHA  Q
Sbjct: 1   MPRFRLDIEYDGSLFAGWQHQADQPSVQQAIEQAIEKFCGEAIRLRAAGRTDAGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DLV+ W    +  A+NA+L+ +   I+IL  ++V   F ARFSAI R YLYRI+ R
Sbjct: 61  VAHVDLVKAWPSDKVRDAVNAHLQAAGARIAILKATVVSDSFDARFSAIGRHYLYRILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +AP AL+KG+ W +PK LD   M  AA+ L+GRHDFTTFRS  CQA+SPIRT++  DV+ 
Sbjct: 121 RAPAALDKGKVWWVPKRLDAGAMHEAAKVLLGRHDFTTFRSTQCQANSPIRTLERLDVSR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G++IE+R  ARSFLH Q+RS VGSLK VGDG W++ DL+ AL+A+DR  CG +APP+GL
Sbjct: 181 QGDMIEVRASARSFLHNQVRSMVGSLKRVGDGGWSAADLKTALEARDRAACGQVAPPDGL 240

Query: 240 YFDSVEY 246
           +   V+Y
Sbjct: 241 FLTGVDY 247


>gi|6685124|gb|AAF23795.1|AF213822_10 tRNA-pseudouridine synthase I [Zymomonas mobilis subsp. mobilis
           ZM4]
          Length = 245

 Score =  274 bits (701), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 132/246 (53%), Positives = 171/246 (69%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +E++G  + GWQR+K+G++IQGSIE+A   + G+   V  AGRTD+GVH L  
Sbjct: 1   MNRYRLTVEFDGRNFMGWQRKKHGATIQGSIEEAGASIAGQPTPVQAAGRTDAGVHGLAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AH D+ R++ P  L +ALNA LK    I+IL+   VD ++HARFS I R YLYRII R+
Sbjct: 61  TAHIDVARDFTPFRLMEALNARLK-PRPIAILSCEQVDPEWHARFSCIGRRYLYRIINRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL LE GRAW + K LD E M IAA+ L+G HDFTTFRS+HCQ+ SP++T+DH DV   
Sbjct: 120 PPLTLEAGRAWHVIKPLDAETMDIAAKRLIGLHDFTTFRSVHCQSKSPVKTLDHLDVRRI 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ IEI   ARSFLH Q+RS VG L LVG G+WT+ D+  AL+A++R   G  APP+GLY
Sbjct: 180 GDQIEITAAARSFLHHQVRSMVGCLVLVGQGQWTADDMTTALEARNRAALGFNAPPDGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FTQAIY 245


>gi|154250719|ref|YP_001411543.1| tRNA pseudouridine synthase A [Parvibaculum lavamentivorans DS-1]
 gi|171769555|sp|A7HPQ3|TRUA_PARL1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|154154669|gb|ABS61886.1| tRNA pseudouridine synthase A [Parvibaculum lavamentivorans DS-1]
          Length = 246

 Score =  274 bits (700), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 129/247 (52%), Positives = 172/247 (69%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+GS + GWQ Q NG S+Q  +E+ I    G+ + + GAGRTD+GVHAL Q
Sbjct: 1   MPRYKLTIEYDGSPFVGWQAQTNGRSVQQVLEEGIKGFCGQELKIFGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D      P  L  A+NA+++    ++I+    V   F ARFSA++R Y+YRI+ R+
Sbjct: 61  VAHVDFETPVAPDTLRDAVNAHMR-PHPVAIVEAEEVPDSFEARFSAVKRHYMYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL L++G+AWL+ K+LD + M  AAQ LVG HDFTTFRS+ CQA SP++T+D   V+ +
Sbjct: 120 APLTLDRGQAWLVHKTLDADAMHDAAQALVGNHDFTTFRSVQCQAKSPVKTVDEISVSRY 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + IEI   ARSFLH Q+RSFVG+LK+VGDG WT   +EKAL A+DR  CGP+APP+GLY
Sbjct: 180 ADEIEIVCRARSFLHNQVRSFVGTLKMVGDGSWTRRKVEKALAAKDRAACGPVAPPDGLY 239

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 240 LLQVDYE 246


>gi|323135724|ref|ZP_08070807.1| tRNA pseudouridine synthase A [Methylocystis sp. ATCC 49242]
 gi|322398815|gb|EFY01334.1| tRNA pseudouridine synthase A [Methylocystis sp. ATCC 49242]
          Length = 245

 Score =  271 bits (692), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 136/246 (55%), Positives = 172/246 (69%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQRQ NG S+Q  +E+A+  + G   V+HGAGRTD+GVHAL Q
Sbjct: 1   MPRYALTIEYDGGPFVGWQRQANGVSVQQRLEEAVAAINGARAVIHGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL REW    L  ALNA+LK  D +++++   VD+ F ARFSAIRR Y Y I  R+
Sbjct: 61  VAHVDLAREWRADRLRDALNAHLK-PDPVAVVSARAVDENFEARFSAIRRHYRYVIDNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL +  GRAW + + LD + M  AAQ LVGRHDFTTFR+  CQA+SP+RT++  DV   
Sbjct: 120 APLTVGLGRAWHVKRPLDAQAMHDAAQRLVGRHDFTTFRASECQANSPVRTLERLDVRRE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ IEI   ARSFLH Q+RS  GSL+ VG GKWT+ DL  AL+A+DR  CG +APP GLY
Sbjct: 180 GDRIEIVTCARSFLHNQVRSMAGSLEHVGSGKWTADDLAAALEAKDRARCGQVAPPHGLY 239

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 240 LVAVDY 245


>gi|260461124|ref|ZP_05809373.1| tRNA pseudouridine synthase A [Mesorhizobium opportunistum WSM2075]
 gi|259033158|gb|EEW34420.1| tRNA pseudouridine synthase A [Mesorhizobium opportunistum WSM2075]
          Length = 249

 Score =  271 bits (692), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 131/248 (52%), Positives = 173/248 (69%), Gaps = 1/248 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IEY+GS + GWQ Q +  S+Q +IE+AI    GE V +  AGRTD+GVHA  Q
Sbjct: 1   MPRFRLDIEYDGSLFAGWQHQADQPSVQQAIEEAIEKFCGEAVRLRAAGRTDAGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DLV+ W    +  A+NA+L+ +   + IL   +V   F ARFSA  R YLYRI+ R
Sbjct: 61  VAHVDLVKAWPGDKVRDAVNAHLQAAGARVVILKAGVVPDDFDARFSATGRHYLYRILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +AP ALEKG+ W +PK LD   M  AA+ L+GRHDFTTFRS  CQA+SP+RT++  DV+ 
Sbjct: 121 RAPSALEKGKVWWVPKRLDAGAMHEAAKILLGRHDFTTFRSTQCQANSPVRTLEQLDVSR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G++IE+R  ARSFLH Q+RS VGSLK VGDG W++ D + AL+A+DR  CG +APP+GL
Sbjct: 181 QGDMIEVRASARSFLHNQVRSMVGSLKRVGDGSWSANDFKAALEARDRAACGQVAPPDGL 240

Query: 240 YFDSVEYS 247
           +   V+YS
Sbjct: 241 FLIGVDYS 248


>gi|13474062|ref|NP_105630.1| tRNA pseudouridine synthase A [Mesorhizobium loti MAFF303099]
 gi|30913408|sp|Q98D55|TRUA_RHILO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|14024814|dbj|BAB51416.1| tRNA-pseudouridine synthase [Mesorhizobium loti MAFF303099]
          Length = 248

 Score =  270 bits (691), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 131/247 (53%), Positives = 173/247 (70%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IEY+GS + GWQ Q +  S+Q +IE+AI    GE V +  AGRTD+GVHA  Q
Sbjct: 1   MPRFRLDIEYDGSLFAGWQHQADQPSVQQAIEQAIEKFCGEAVRLRAAGRTDAGVHASAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL + W    +  A+NA+L+ +   ++IL  +IV   F ARFSA  R YLYRI+ R
Sbjct: 61  VAHVDLAKPWPGDKVRDAVNAHLQAAGAHVAILKAAIVPDDFDARFSATGRHYLYRILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +AP ALEKG+ W +PK LD   M  AA+ L+GRHDFTTFRS  CQA+SP+RT++  DV+ 
Sbjct: 121 RAPAALEKGKVWWVPKRLDAGAMHEAAKLLLGRHDFTTFRSTQCQANSPVRTLERLDVSR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G++IE+R  ARSFLH Q+RS VGSLK VGDG WT  +L+ AL+A+DR  CG +APP+GL
Sbjct: 181 AGDMIEVRASARSFLHNQVRSMVGSLKRVGDGGWTEAELKAALEARDRAACGQVAPPDGL 240

Query: 240 YFDSVEY 246
           +   V+Y
Sbjct: 241 FLIGVDY 247


>gi|299132601|ref|ZP_07025796.1| tRNA pseudouridine synthase A [Afipia sp. 1NLS2]
 gi|298592738|gb|EFI52938.1| tRNA pseudouridine synthase A [Afipia sp. 1NLS2]
          Length = 245

 Score =  269 bits (688), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 130/246 (52%), Positives = 171/246 (69%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +IIEY+G+ + GWQ Q NG S+QG++E A+  +TG  V VHGAGRTD+GVHAL Q
Sbjct: 1   MPRYKLIIEYDGTPFCGWQYQDNGPSVQGALEDAVMAMTGSRVRVHGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL + +    +  ALNA+++    I +L+  IV   F ARFSA++R Y+YRI  R+
Sbjct: 61  VAHIDLEKTYRADRVRDALNAHVR-PHPIGVLSAEIVPDTFEARFSALKRHYIYRISNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A LAL+ GRAW + + LD   M  AAQ L+G+HDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 ANLALDAGRAWRVARPLDVAAMNEAAQVLIGKHDFTTFRDTECQAKSPDKTLDQLDVIRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARSFLH+Q+RS VGSL  VG G+WT+ D+ KAL A++R  CGP+APP+GLY
Sbjct: 180 GDTVNIVTSARSFLHSQVRSMVGSLVWVGHGRWTAADMRKALDARNRAACGPVAPPDGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVKVDY 245


>gi|319407940|emb|CBI81594.1| tRNA pseudouridine synthase A [Bartonella schoenbuchensis R1]
          Length = 247

 Score =  268 bits (686), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 129/247 (52%), Positives = 169/247 (68%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R+ + +EY+GS Y GWQRQ    +IQG+IE+AIF  +GE + +  AGRTD+GVHA+ Q
Sbjct: 1   MVRFKLTLEYDGSNYAGWQRQAGLRTIQGAIEQAIFNFSGEKLTIVTAGRTDAGVHAIEQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W    +  ALNA+L+   + I++LN+  V   FHARF A +R YL++I+ R
Sbjct: 61  VAHVDFTKNWHANTVHNALNAHLQQQGENIAVLNVQNVPDSFHARFCATKRYYLFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++P AL   R W +PK L+ + M  AAQ LVG+HDFTTFRS HCQA SPIRT++  DV  
Sbjct: 121 RSPPALNVKRVWWLPKHLNADAMHEAAQKLVGQHDFTTFRSAHCQAKSPIRTLERLDVYR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I +   ARSFLH QIRSF GSL  VG G+WT+ DLE AL A+DR  CG +APP GL
Sbjct: 181 KGEEIFLYAQARSFLHHQIRSFAGSLVKVGTGQWTAQDLEAALNAKDRARCGMVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   ++Y
Sbjct: 241 YLMKIDY 247


>gi|319403559|emb|CBI77141.1| tRNA pseudouridine synthase A [Bartonella rochalimae ATCC BAA-1498]
          Length = 247

 Score =  268 bits (685), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 129/247 (52%), Positives = 170/247 (68%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R+ + +EY+GS Y GWQRQKN  +IQGSIE AIF  +G+ + +  AGRTD+GVHA+ Q
Sbjct: 1   MVRFKLTLEYDGSNYAGWQRQKNLRTIQGSIENAIFHFSGQKLTITTAGRTDAGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W    +  ALNA+L K  + I++LN+  V   F ARF A +R YL++I+ R
Sbjct: 61  VAHIDFEKNWNTNTVRDALNAHLQKQGEDIAVLNVQNVPDNFDARFCATKRHYLFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++P AL   R W +PK LD + M  AAQ LVG+HDFTTFRS +CQA SP+RT++  D+  
Sbjct: 121 RSPPALNTKRVWWLPKPLDADAMHKAAQKLVGQHDFTTFRSAYCQAKSPVRTLERLDIQR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ I +   ARSFLH QIRSF GSL  VG G+WT+ DLE AL A++R  CG +APP GL
Sbjct: 181 EGDEIFLYAQARSFLHHQIRSFAGSLMEVGIGRWTAEDLEAALHARNRARCGVVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLMKVDY 247


>gi|90419798|ref|ZP_01227707.1| tRNA pseudouridine synthase A [Aurantimonas manganoxydans SI85-9A1]
 gi|90335839|gb|EAS49587.1| tRNA pseudouridine synthase A [Aurantimonas manganoxydans SI85-9A1]
          Length = 259

 Score =  268 bits (685), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 136/247 (55%), Positives = 167/247 (67%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IEY+G+ Y GWQRQK   S Q  IE A+   TGE   +  AGRTD+GVHA  Q
Sbjct: 1   MPRFKLTIEYDGTPYCGWQRQKTDLSAQEVIETAVEGFTGEAATLFAAGRTDAGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R+W P  +  ALNA+L+ +  ++IL+   V   F ARFSA +R YLYRI  R+
Sbjct: 61  VAHVDLRRDWEPDTVRDALNAHLRDA-PVAILSAERVADDFDARFSARKRFYLYRIFNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNS 179
           AP AL  GR W + K LD + M  AAQ LVG HDF TFRS HCQA +PIRT++  D V  
Sbjct: 120 APTALLIGRVWWVSKPLDVDAMHAAAQRLVGTHDFDTFRSAHCQAKNPIRTLEQLDVVRG 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I I  +A+SFLH QIRSF GSLKLVG+G W++ DL  AL+A+DRK CGP+APP+GL
Sbjct: 180 PGEEIHIHAMAQSFLHNQIRSFAGSLKLVGEGHWSAADLVAALEARDRKRCGPVAPPDGL 239

Query: 240 YFDSVEY 246
           Y   VEY
Sbjct: 240 YLTRVEY 246


>gi|319404987|emb|CBI78590.1| tRNA pseudouridine synthase A [Bartonella sp. AR 15-3]
          Length = 247

 Score =  268 bits (684), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 130/247 (52%), Positives = 169/247 (68%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+GS Y GWQRQK+  +IQGSIEKA+F  +G+ + +  AGRTD+GVHA+ Q
Sbjct: 1   MARFKLTLEYDGSNYAGWQRQKSLRTIQGSIEKAVFHFSGQKLTITTAGRTDAGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W   I+  ALNA+L K  + I +LN+  V   F ARF A +R YL++I+ R
Sbjct: 61  VAHIDFEKHWNTHIVRDALNAHLQKQGEDIVVLNVQSVPDNFDARFCATKRHYLFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++P AL   R W +PK LD + M  AAQ LVG+HDFTTFRS HCQA SP+RT++  D+  
Sbjct: 121 RSPPALNAKRVWWLPKPLDADAMHKAAQRLVGQHDFTTFRSAHCQAKSPVRTLERLDIQR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I +   ARSFLH QIRSF GSL  VG G+WT+ DLE AL A++R  CG +APP GL
Sbjct: 181 EGEEIVLYAQARSFLHHQIRSFAGSLMEVGIGRWTAEDLEAALHAKNRARCGVVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLIKVDY 247


>gi|153008677|ref|YP_001369892.1| tRNA pseudouridine synthase A [Ochrobactrum anthropi ATCC 49188]
 gi|166228741|sp|A6WYK9|TRUA_OCHA4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|151560565|gb|ABS14063.1| tRNA pseudouridine synthase A [Ochrobactrum anthropi ATCC 49188]
          Length = 251

 Score =  268 bits (684), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 129/248 (52%), Positives = 171/248 (68%), Gaps = 1/248 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ Y GWQRQ+NG ++Q +IE A     GE + +  AGRTD+GVHA  Q
Sbjct: 1   MPRYKLTVEYDGTPYVGWQRQENGHAVQNAIELAFKKFCGEDLTLSAAGRTDAGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H DL ++W    +  A+NA+L ++D  +SILN+      F ARFSA  R YLYRI  R
Sbjct: 61  VVHVDLTKDWGAGKVRDAVNAHLVMADERVSILNVERTTDTFDARFSARARHYLYRIHNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLA++  RAW + K LD E M  AA+ L+G HDFTTFR+  CQA SP++T+D  DV  
Sbjct: 121 RAPLAVDYQRAWWVQKRLDAEAMHEAAKRLLGEHDFTTFRATQCQAKSPVKTLDRLDVIR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +E+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+A+DRK CG +APP GL
Sbjct: 181 NGDYVEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALEAKDRKACGQVAPPYGL 240

Query: 240 YFDSVEYS 247
           Y   V+Y+
Sbjct: 241 YLIGVDYA 248


>gi|49473750|ref|YP_031792.1| tRNA pseudouridine synthase A [Bartonella quintana str. Toulouse]
 gi|51316599|sp|Q6G1G9|TRUA_BARQU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|49239253|emb|CAF25574.1| tRNA pseudouridine synthase A [Bartonella quintana str. Toulouse]
          Length = 247

 Score =  267 bits (683), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 132/247 (53%), Positives = 167/247 (67%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+GS Y GWQRQ    +IQ ++E+AIF  +G+ +    AGRTD+GVHA  Q
Sbjct: 1   MPRFKLTLEYDGSNYAGWQRQAELHTIQSALEQAIFHFSGQQLTTTTAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D ++ W    +  ALNAYL K  + I++LN+  V   F ARFSAI+R YL++I+ R
Sbjct: 61  VAHVDFIKNWQTYTVRDALNAYLQKQGEEIAVLNVQNVPDNFDARFSAIKRHYLFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            +P AL   R W IPK L+ + M  AAQ LVG+HDFTTFRS HCQA SPIRT++  DV  
Sbjct: 121 LSPPALNIKRVWWIPKPLNVDAMHQAAQKLVGQHDFTTFRSAHCQAKSPIRTLERLDVYR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I +   ARSFLH QIRSF GSL  VG G+WT+ DLE AL A+DRK CG +APP GL
Sbjct: 181 EGEEIFLYAQARSFLHHQIRSFAGSLMEVGIGRWTAQDLEAALHAKDRKRCGMVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLTQVDY 247


>gi|296446982|ref|ZP_06888917.1| tRNA pseudouridine synthase A [Methylosinus trichosporium OB3b]
 gi|296255549|gb|EFH02641.1| tRNA pseudouridine synthase A [Methylosinus trichosporium OB3b]
          Length = 246

 Score =  267 bits (683), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 136/247 (55%), Positives = 173/247 (70%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R+ +IIEY+G  + GWQRQ+NG SIQ  +E+A+  L +G   VVHGAGRTD+GVHAL 
Sbjct: 1   MPRFALIIEYDGGPFVGWQRQENGVSIQQRLEEAVAALESGARRVVHGAGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAH DL R+W    L  A+NA+L+  D I++L    V + F ARFSA+RR Y Y I  R
Sbjct: 61  QVAHVDLTRDWRADRLRDAINAHLR-PDPIAVLEARGVAEGFEARFSAVRRHYRYIIDNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APL L++GR W + + LD   M  AAQ LVGRHDFTTFRS  CQA SPIRT++  DV  
Sbjct: 120 RAPLTLQRGRMWHVKRPLDAAAMHAAAQLLVGRHDFTTFRSTECQAESPIRTLERLDVRR 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LIEI   ARSFLH Q+RS  GSL+ VG G+W++ DL  AL+A++R  CG +APP GL
Sbjct: 180 EGSLIEITTSARSFLHNQVRSLAGSLEHVGSGRWSAADLRAALEARERARCGQVAPPHGL 239

Query: 240 YFDSVEY 246
           Y  +V+Y
Sbjct: 240 YLVAVDY 246


>gi|319406472|emb|CBI80113.1| tRNA pseudouridine synthase A [Bartonella sp. 1-1C]
          Length = 247

 Score =  267 bits (683), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 129/247 (52%), Positives = 169/247 (68%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+GS Y GWQRQKN  +IQGSIE AIF  +G+ + +  AGRTD+GVHA+ Q
Sbjct: 1   MARFKLTLEYDGSNYAGWQRQKNLRTIQGSIENAIFHFSGQKLTITTAGRTDAGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W    +  ALNA+L K  + I++LN+  V   F ARF A +R YL++I+ R
Sbjct: 61  VAHIDFEKNWNTNTVRDALNAHLQKQGENIAVLNVQNVPDNFDARFCATKRHYLFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++P AL   R W +PK LD + M  AAQ LVG+HDFTTFRS +CQA SP+RT++  D+  
Sbjct: 121 RSPPALNTKRVWWLPKPLDADAMHKAAQKLVGQHDFTTFRSAYCQAKSPVRTLERLDIQR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ I +   ARSFLH QIRSF GSL  VG G+WT+ DLE AL A++R  CG +APP GL
Sbjct: 181 EGDEIFLYAQARSFLHHQIRSFAGSLMEVGIGRWTAEDLEAALHARNRARCGVVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLMKVDY 247


>gi|288959244|ref|YP_003449585.1| tRNA pseudouridine synthase A [Azospirillum sp. B510]
 gi|288911552|dbj|BAI73041.1| tRNA pseudouridine synthase A [Azospirillum sp. B510]
          Length = 245

 Score =  266 bits (681), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 123/246 (50%), Positives = 175/246 (71%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+G  + GWQRQ NG S+Q S+E+A+  ++GE+  VHG+GRTD+GVHAL Q
Sbjct: 1   MQRWKLTVEYDGRPFVGWQRQDNGPSVQQSLEEAVRRLSGEVARVHGSGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFDL + +  + L  ALN +LK +  I++L +  V + FHAR ++  R+Y+YRI+ R+
Sbjct: 61  VCHFDLEKPFTALKLRDALNFHLKPA-PIAVLEVEAVTEDFHARLTSTGRAYVYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APLALE GRAW + + LD + M  AAQ LVG+HDF++FR+  CQA SP++T+D   V   
Sbjct: 120 APLALESGRAWHVTRPLDADAMHAAAQVLVGQHDFSSFRAALCQAKSPVKTLDRLAVERQ 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I +   ARSFLH Q+R+ VG+L+LVG GKWT+ D+ +AL+A DR + GP  PP+GLY
Sbjct: 180 GDEIRVHAAARSFLHHQVRNMVGTLELVGAGKWTADDVRRALEACDRAKAGPTCPPDGLY 239

Query: 241 FDSVEY 246
           F +  Y
Sbjct: 240 FLAARY 245


>gi|49474896|ref|YP_032937.1| tRNA pseudouridine synthase A [Bartonella henselae str. Houston-1]
 gi|51316603|sp|Q6G547|TRUA_BARHE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|49237701|emb|CAF26890.1| tRNA pseudouridine synthase A [Bartonella henselae str. Houston-1]
          Length = 247

 Score =  266 bits (681), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 131/247 (53%), Positives = 167/247 (67%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+GS Y GWQRQ    +IQ ++E+A+F  +G+ + +  AGRTD+GVHA  Q
Sbjct: 1   MPRFKLTLEYDGSNYAGWQRQAELRTIQSALEQALFHFSGQQLTITTAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W    +  ALNA+L K  D I+IL++  V   F ARFSAI+R YL++I+ R
Sbjct: 61  VAHVDFEKNWRTHTVRDALNAHLQKQGDNIAILHVQNVPDSFDARFSAIKRHYLFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++P AL   R W IPK L+ + M  AAQ LVG+HDFTTFRS HCQA SPIRT++  DV  
Sbjct: 121 RSPPALNTKRVWWIPKPLNAQAMHEAAQKLVGKHDFTTFRSAHCQAKSPIRTLERLDVQR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I +   ARSFLH QIRSF GSL  VG G+WT+ DLE AL A+DR  CG +APP GL
Sbjct: 181 EGEEIFLYAQARSFLHHQIRSFAGSLMEVGIGRWTTQDLEAALHAKDRTRCGMVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   VEY
Sbjct: 241 YLTKVEY 247


>gi|75677245|ref|YP_319666.1| tRNA pseudouridine synthase A [Nitrobacter winogradskyi Nb-255]
 gi|123759229|sp|Q3SN27|TRUA_NITWN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|74422115|gb|ABA06314.1| tRNA pseudouridine synthase [Nitrobacter winogradskyi Nb-255]
          Length = 255

 Score =  266 bits (680), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 129/247 (52%), Positives = 167/247 (67%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQ Q NG S+QG++E A+  + G+ V VHGAGRTD+GVHAL Q
Sbjct: 1   MPRYKLTIEYDGGPFCGWQYQTNGPSVQGALEAAVKAICGDDVRVHGAGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ R ++P  L   LNA+L+    I +L   IV   F ARFSA RR Y+YRI  R+
Sbjct: 61  VAHCDIARHFMPDRLRDGLNAHLR-PHPIGVLEAEIVPDSFEARFSARRRHYIYRIANRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A LA++ GR W +P+ LD E M  AAQ L+G+HDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 ANLAIDVGRVWRVPRPLDTEAMHAAAQRLLGKHDFTTFRDTECQAKSPEKTLDQLDVIRN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARS+LH+Q+RS VGSL  VG G+W + DL  AL A+ R+ CGP+APP+GLY
Sbjct: 180 GDNVSIITSARSYLHSQVRSMVGSLVWVGHGRWNADDLSGALAARRREACGPVAPPDGLY 239

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 240 LARVDYE 246


>gi|85713817|ref|ZP_01044807.1| tRNA pseudouridine synthase A [Nitrobacter sp. Nb-311A]
 gi|85699721|gb|EAQ37588.1| tRNA pseudouridine synthase A [Nitrobacter sp. Nb-311A]
          Length = 245

 Score =  266 bits (679), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 128/246 (52%), Positives = 168/246 (68%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQ Q NG S+QG++E A+  + G+ V VHGAGRTD+GVHAL Q
Sbjct: 1   MPRYRLTIEYDGGPFCGWQYQDNGPSVQGALEAAVKAICGDCVRVHGAGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + + P  L   LNA+L+    I +L   IV   F ARFSA RR Y+YRI  R+
Sbjct: 61  VAHCDIAKHFAPDRLRDGLNAHLR-PHPIGVLEAEIVPDSFEARFSARRRHYIYRIANRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A LA++ GR W +P+ LD E M  AAQ L+G+HDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 ANLAIDVGRVWRVPRPLDTEAMHDAAQRLLGKHDFTTFRDTECQAKSPEKTLDQLDVVRN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I  +ARS+LH+Q+RS VGSL  VG G+W++ DL  AL A+ R+ CGP+APP+GLY
Sbjct: 180 GDNVSIITLARSYLHSQVRSMVGSLVWVGHGRWSADDLSSALAARRREACGPVAPPDGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVRVDY 245


>gi|319898267|ref|YP_004158360.1| tRNA pseudouridine synthase A [Bartonella clarridgeiae 73]
 gi|319402231|emb|CBI75764.1| tRNA pseudouridine synthase A [Bartonella clarridgeiae 73]
          Length = 247

 Score =  265 bits (677), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 131/247 (53%), Positives = 166/247 (67%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+GS Y GWQRQ N  +IQGSIE+AIF  +G+ + +  AGRTD+GVHA  Q
Sbjct: 1   MARFKLTLEYDGSNYAGWQRQANLRTIQGSIEQAIFHFSGQKLTITTAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  + W    +  ALNA+L K  + ISILN+  V   F ARF A +R YL++I+ R
Sbjct: 61  VAHIDFEKNWNTHTVRDALNAHLQKQGEDISILNVQNVPDNFDARFCATKRHYLFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++P  L   R W +PK LD + M  AAQ LVG+HDFTTFRS HCQA SPIRT++  D+  
Sbjct: 121 RSPPVLNAKRVWWLPKPLDADAMHKAAQRLVGQHDFTTFRSAHCQAKSPIRTLERLDIQR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I +   ARSFLH QIRSF GSL  VG G+WT+ DLE AL A++R  CG +APP GL
Sbjct: 181 KGEEIFLYAQARSFLHHQIRSFAGSLMEVGIGRWTAEDLEAALHAKNRARCGVVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLIKVDY 247


>gi|121602227|ref|YP_989569.1| tRNA pseudouridine synthase A [Bartonella bacilliformis KC583]
 gi|166228679|sp|A1UUB6|TRUA_BARBK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120614404|gb|ABM45005.1| tRNA pseudouridine synthase A [Bartonella bacilliformis KC583]
          Length = 247

 Score =  265 bits (677), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 127/247 (51%), Positives = 169/247 (68%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+GS Y GWQRQ    ++QG++E+AIF  +G+ + +  AGRTD+GVHA  Q
Sbjct: 1   MARFKLTLEYDGSNYAGWQRQAELRTVQGAVEQAIFHFSGQQLTITTAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKIS-DTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH D  ++W    +  ALNA+L+   D I+ILN+  +   F AR SA++R YL++I+ R
Sbjct: 61  VAHVDFEKDWHVNTIHNALNAHLRQQGDNIAILNVENIPDSFDARLSAVKRHYLFKILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +AP AL   R W +P+ L+ + M  AAQ LVG+HDFTTFRS HCQA SPIRT++  DV  
Sbjct: 121 RAPPALNAKRVWWLPRPLNADAMHKAAQKLVGKHDFTTFRSAHCQAKSPIRTLECLDVQR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I +   ARSFLH QIRSF GSL  VG G+WT+ DLE+AL A+DR  CG +APP GL
Sbjct: 181 EGEEIFLYARARSFLHHQIRSFAGSLMEVGIGRWTAQDLEEALHAKDRARCGMVAPPSGL 240

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 241 YLTQVDY 247


>gi|209886648|ref|YP_002290505.1| tRNA pseudouridine synthase A [Oligotropha carboxidovorans OM5]
 gi|229557998|sp|B6JJP6|TRUA_OLICO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|209874844|gb|ACI94640.1| tRNA pseudouridine synthase A [Oligotropha carboxidovorans OM5]
          Length = 245

 Score =  265 bits (677), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 131/246 (53%), Positives = 169/246 (68%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY+G+ + GWQ Q NG S+QG++E A+  + G  V VHGAGRTD+GVHAL Q
Sbjct: 1   MPRYKLLIEYDGTPFCGWQYQDNGPSVQGALEDAVAALAGTHVRVHGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL + +    +  ALNA+L+    I +L+  IV + F +RFSA++R Y+YRI  R+
Sbjct: 61  VAHIDLEKSYRTDQVRDALNAHLR-PHPIGVLSAEIVPETFESRFSAVKRHYIYRISNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A LAL+  RAW I ++LD   M  AAQ LVGRHDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 ANLALDLHRAWRIARTLDVAAMHEAAQVLVGRHDFTTFRDTECQAKSPEKTLDQLDVTRE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARSFLH+Q+RS VGSL  VG G+WT  D+  AL A+DR  CGP+APPEGLY
Sbjct: 180 GDAVSIVTSARSFLHSQVRSMVGSLVWVGHGRWTIADMRNALAARDRTACGPVAPPEGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVRVDY 245


>gi|114568998|ref|YP_755678.1| tRNA pseudouridine synthase A [Maricaulis maris MCS10]
 gi|122316778|sp|Q0ASJ7|TRUA_MARMM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|114339460|gb|ABI64740.1| tRNA pseudouridine synthase A [Maricaulis maris MCS10]
          Length = 249

 Score =  264 bits (675), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 124/246 (50%), Positives = 170/246 (69%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQRQ N  S+Q S+E+A   + G  V+V+GAGRTDSGVHAL Q
Sbjct: 1   MPRYRITIEYDGRPFSGWQRQDNAPSVQESLERAAEKLDGAPVLVYGAGRTDSGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++     +  A+N +LK  D ++++  + V   FHARFSA RR YLYR+I R+
Sbjct: 61  VAHLDLAKDLSTDKVRDAINYHLK-PDPVAVIEAARVSDDFHARFSATRRHYLYRMIDRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL L++G+ W + + LD E M  AAQ L+G+HDFTTFR   CQA SP++++D   V+ +
Sbjct: 120 APLTLDRGQVWRVTRKLDAEAMHHAAQALLGQHDFTTFRDAQCQAESPVKSLDAISVSRY 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +++   ARSFLH Q+RS VGSL  VG GKW++ D ++AL A DR  CGP+AP +GLY
Sbjct: 180 GEEVQLTCSARSFLHRQVRSMVGSLVEVGVGKWSARDFKRALDAADRSRCGPVAPADGLY 239

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 240 LTAVDY 245


>gi|83594681|ref|YP_428433.1| pseudouridylate synthase [Rhodospirillum rubrum ATCC 11170]
 gi|123725839|sp|Q2RNZ9|TRUA_RHORT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|83577595|gb|ABC24146.1| Pseudouridylate synthase [Rhodospirillum rubrum ATCC 11170]
          Length = 278

 Score =  263 bits (672), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 126/246 (51%), Positives = 168/246 (68%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RY + +EY+G GY GWQRQ NG +IQ S+E+A F + G    VHG+GRTDSGVHAL Q
Sbjct: 1   MVRYRLTVEYDGRGYCGWQRQDNGPTIQQSLEEAAFRLCGVATRVHGSGRTDSGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R +    + KALNA+L+    I++++ + V + FHARFSA  RSY YRI+ R 
Sbjct: 61  VAHLDLPRAYGAATVMKALNAHLR-PQPIAVIDAAEVAEDFHARFSAEERSYRYRILNRI 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP  L++GR W + + ++   M  AAQ LVGRHDF++FR+  CQA SP++T+    V   
Sbjct: 120 APPTLDQGRVWWVARPMEAAIMDEAAQVLVGRHDFSSFRAAECQADSPVKTLSELRVTRV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I +   ARSFLH Q+R+ VG+L LVGDG+WT+  L  AL+A DR   GP APP+GLY
Sbjct: 180 GDEIHVFARARSFLHHQVRNMVGTLALVGDGRWTADRLRAALEACDRSAAGPTAPPDGLY 239

Query: 241 FDSVEY 246
           F  V +
Sbjct: 240 FLRVRF 245


>gi|92119152|ref|YP_578881.1| tRNA pseudouridine synthase A [Nitrobacter hamburgensis X14]
 gi|123264920|sp|Q1QH76|TRUA_NITHX RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91802046|gb|ABE64421.1| tRNA pseudouridine synthase A [Nitrobacter hamburgensis X14]
          Length = 245

 Score =  263 bits (671), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 126/246 (51%), Positives = 165/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQ Q NG S+QG++E A+  + G+ V VHGAGRTD+GVHAL Q
Sbjct: 1   MPRYKLTIEYDGGPFCGWQYQDNGPSVQGALEAAVKAICGDAVRVHGAGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + + P  L   LNA+L+    I +L   IV   F ARFSA+RR Y+YRI  R+
Sbjct: 61  VAHCDIAKHFAPNRLRDGLNAHLR-PHPIGVLTAEIVPDTFEARFSALRRHYVYRIANRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A LA++ G  W +P+ LD   M  AAQ L+G+HDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 ANLAIDVGHVWRVPRPLDTLAMHAAAQRLIGKHDFTTFRDTECQAKSPEKTLDQLDVVRN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARSFLH+Q+RS VGSL  VG G+W++ DL  AL  + R+ CGP+APP+GLY
Sbjct: 180 GDTVTIVTSARSFLHSQVRSMVGSLVWVGHGRWSADDLSNALAERRREACGPVAPPDGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVRVDY 245


>gi|85707833|ref|ZP_01038899.1| tRNA pseudouridine synthase A [Erythrobacter sp. NAP1]
 gi|85689367|gb|EAQ29370.1| tRNA pseudouridine synthase A [Erythrobacter sp. NAP1]
          Length = 247

 Score =  262 bits (670), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 127/246 (51%), Positives = 167/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IE++G+ + G QRQK+G S+Q SIE+A+  +TGE   +H AGRTD+GVHAL  
Sbjct: 1   MTRFALTIEFDGTPFQGLQRQKHGPSVQQSIEEALHRITGEDATLHSAGRTDTGVHALGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +H DL ++  P  L +ALNA+L+  D I+IL   +VD+ +HARFS + R Y+Y+I  R+
Sbjct: 61  RSHVDLEKDIDPFRLSEALNAHLR-PDPIAILACEVVDEDWHARFSCVGRRYVYKIANRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL L K RAW +   LD E M  AAQ LVGRHDFTTFRS+HCQA  P++T+D  +V   
Sbjct: 120 APLTLAKNRAWQVAHDLDHEAMHRAAQALVGRHDFTTFRSVHCQAKDPVKTLDQLNVERV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I   ARSFLH Q+RS VG LKLVG G W    + +AL A+DR + G  APP+GLY
Sbjct: 180 GDEIHIHAAARSFLHHQVRSMVGCLKLVGAGSWREEQVAEALAAKDRSKLGLNAPPQGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FVEATY 245


>gi|298293826|ref|YP_003695765.1| tRNA pseudouridine synthase A [Starkeya novella DSM 506]
 gi|296930337|gb|ADH91146.1| tRNA pseudouridine synthase A [Starkeya novella DSM 506]
          Length = 250

 Score =  261 bits (668), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 129/251 (51%), Positives = 169/251 (67%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q  G+S+QG++ +A+  +TGE V VHGAGRTD+GVHA  Q
Sbjct: 1   MPRYKLTIEYDGTPFVGWQIQAEGTSVQGALAQAVTRLTGEQVAVHGAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH +L R+W P  +  ALNA+L+    I++L+       FHARFSA  R Y+YRII R+
Sbjct: 61  VAHVELSRDWRPDTVRDALNAHLR-PHPIAVLSAERAADDFHARFSATGRRYVYRIIARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             LALE+ RAW + + LD   M   A  LVGRHDFTTFR++ CQA+SP++T+D  +V   
Sbjct: 120 PDLALERNRAWRVLRPLDVAGMAEGAARLVGRHDFTTFRAVGCQAASPLKTLDRLEVEEV 179

Query: 181 ---GNLIEIRV--VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              G  +EIRV   ARSFLH Q+RS VG+L  VG+G WT  D+  AL+A+DR  CGP+AP
Sbjct: 180 ALEGPGMEIRVHAAARSFLHHQVRSMVGTLVKVGEGAWTPDDVTAALEAKDRTRCGPMAP 239

Query: 236 PEGLYFDSVEY 246
             GLY   V Y
Sbjct: 240 SAGLYLAEVTY 250


>gi|84683526|ref|ZP_01011429.1| tRNA pseudouridine synthase A [Maritimibacter alkaliphilus
           HTCC2654]
 gi|84668269|gb|EAQ14736.1| tRNA pseudouridine synthase A [Rhodobacterales bacterium HTCC2654]
          Length = 257

 Score =  261 bits (666), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 123/250 (49%), Positives = 170/250 (68%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQRQK+  S+QG++E A+  +  ++  +  AGRTD+GVHAL Q
Sbjct: 1   MPRYALKIEYDGRPFSGWQRQKDQPSVQGAVEAALGKLEADVPSIAAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA  DL ++W P  L +ALN +LK  D ++I+  ++VD  FHARFSAI R YL+R+I+R+
Sbjct: 61  VATCDLQKDWTPFRLTEALNYHLK-PDRVAIVACALVDDGFHARFSAIERQYLFRLISRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL  ++G AW + ++LD + M+  A  L+GRHDFTTFRS  CQA SP++T+D   V + 
Sbjct: 120 APLVHDRGNAWRVVQALDADAMQAGADRLIGRHDFTTFRSTMCQADSPVKTLDELRVETL 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      V ARSFLH Q+RSFVG+L+ VG G W+  D+  AL+A+DR  CGP+ PP
Sbjct: 180 PYPGGTEYRFHVRARSFLHNQVRSFVGTLERVGAGSWSPDDVTAALEARDRAACGPVCPP 239

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 240 DGLYLARVGY 249


>gi|83309340|ref|YP_419604.1| pseudouridylate synthase [Magnetospirillum magneticum AMB-1]
 gi|123768092|sp|Q2WAT0|TRUA_MAGSA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|82944181|dbj|BAE49045.1| Pseudouridylate synthase [Magnetospirillum magneticum AMB-1]
          Length = 256

 Score =  260 bits (665), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 123/247 (49%), Positives = 170/247 (68%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G+ + GWQRQ  G S+QG +EKA+  + G    +H AGRTD+GVHA  Q
Sbjct: 1   MPRYRLLVEYDGTPFNGWQRQDKGLSVQGILEKAVEKLCGVPCTLHAAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R++    +  ALN ++K    ++++   +VD+ FHARFSA+ R+YLYRI+ R+
Sbjct: 61  VAHVDLPRDYPADTVRDALNYHMK-PKPVAVVAAELVDEDFHARFSAVGRAYLYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APLAL++ RAW +P +LD E M   A+ L+G HDF+TFR+  CQA SP++T+D  DV   
Sbjct: 120 APLALDQHRAWWVPVALDAEAMAEGARRLLGHHDFSTFRASECQAKSPMKTLDVLDVTRV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I   ARSFLH Q+R+ VG+LKLVG+GKW+  D+ K L+A+DR + GP AP  GL 
Sbjct: 180 GEEIRIVAEARSFLHHQVRNMVGTLKLVGEGKWSPDDMAKVLEARDRTKGGPTAPAAGLV 239

Query: 241 FDSVEYS 247
              V YS
Sbjct: 240 LTGVSYS 246


>gi|296284450|ref|ZP_06862448.1| tRNA pseudouridine synthase A [Citromicrobium bathyomarinum JL354]
          Length = 258

 Score =  258 bits (659), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 123/244 (50%), Positives = 168/244 (68%), Gaps = 1/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +E++G+ +FG QRQK+G S+Q ++E+A   VTG+ V +H AGRTD+GVHA+   +
Sbjct: 5   RYALTLEFDGTPFFGLQRQKDGPSVQQAVEEAAQAVTGQQVTLHSAGRTDTGVHAIAMRS 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD+  +  P  + +A+NA+L+ +  I++ +   V + +HARFS I R YLYRII R+AP
Sbjct: 65  HFDVESKLTPFRMGEAINAHLRPA-PIAVTHCEAVPEDWHARFSCIGRRYLYRIINRRAP 123

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
           L LEK RAWL+    D E M  AAQ LVG HDFTTFRS+HCQA+SP++T+D  DV   G+
Sbjct: 124 LTLEKNRAWLVSPECDAEAMHRAAQSLVGHHDFTTFRSVHCQAASPVKTLDRLDVERAGD 183

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + V ARSFLH Q+RS VG L LVG G+W    + + L+A+DR+E G  AP  GLYF 
Sbjct: 184 EIRVHVAARSFLHHQVRSMVGCLALVGMGRWNEGRIAQVLEAKDRQELGLNAPSHGLYFV 243

Query: 243 SVEY 246
              Y
Sbjct: 244 EAVY 247


>gi|312113444|ref|YP_004011040.1| tRNA pseudouridine synthase A [Rhodomicrobium vannielii ATCC 17100]
 gi|311218573|gb|ADP69941.1| tRNA pseudouridine synthase A [Rhodomicrobium vannielii ATCC 17100]
          Length = 245

 Score =  258 bits (659), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 129/246 (52%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q NG S+Q  + +AI   TG   +  GAGRTD+GVHA  Q
Sbjct: 1   MPRYKITIEYDGTPFSGWQMQANGRSVQDHLARAIERFTGVRAIPRGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R W P  +  ALN +L+ +  + IL    VD+ F ARFSA  R YLYRI+TR+
Sbjct: 61  VAHVDLERRWPPETVRNALNFHLRPAPMV-ILACEEVDETFDARFSAKARHYLYRIVTRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +PLAL++ RAW I   LD E M+  A+HL+G HDFTTFR+  CQA SP+RT+D   V S 
Sbjct: 120 SPLALDRDRAWHIGVPLDAEAMQEGARHLLGHHDFTTFRASQCQAKSPLRTLDTLTVRSE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I   ARSFLH Q+RS  GSLKLVG+GKW    + +AL+A+DR+ CG +AP  GLY
Sbjct: 180 GESVFIATSARSFLHNQVRSMAGSLKLVGEGKWQPERMREALEARDRRACGSVAPACGLY 239

Query: 241 FDSVEY 246
           F +V+Y
Sbjct: 240 FMTVDY 245


>gi|154247231|ref|YP_001418189.1| tRNA pseudouridine synthase A [Xanthobacter autotrophicus Py2]
 gi|238686729|sp|A7IKI9|TRUA_XANP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|154161316|gb|ABS68532.1| tRNA pseudouridine synthase A [Xanthobacter autotrophicus Py2]
          Length = 245

 Score =  258 bits (659), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 125/246 (50%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ Y GWQ Q +  ++QG++ +A     GE V V GAGRTD+GVHA  Q
Sbjct: 1   MPRYKLTIEYDGTPYAGWQIQADQQTVQGALAQAFKRFCGEDVHVAGAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R W    +  A+ A L+    I++L+   V   F ARFSA +R YLYRII R+
Sbjct: 61  VAHVDLSRHWRSDTVRDAMTAQLR-PHPIAVLSAEEVPDSFDARFSATKRHYLYRIINRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             LAL++ RAW IP+ LD + M  AAQ L+G+HDF+TFR+  CQA+SP++T+D  DV+  
Sbjct: 120 PDLALDRDRAWRIPQKLDAQAMHEAAQRLLGKHDFSTFRAAECQAASPLKTLDQLDVSRS 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I +   ARSFLH Q+RS VGSL  VG+G+W++ DLE AL+A DR  CGP+AP  GLY
Sbjct: 180 GDEIRVITSARSFLHHQVRSMVGSLMRVGEGRWSADDLEAALKAADRTRCGPMAPAAGLY 239

Query: 241 FDSVEY 246
             +V Y
Sbjct: 240 LAAVSY 245


>gi|114706822|ref|ZP_01439722.1| tRNA pseudouridine synthase A [Fulvimarina pelagi HTCC2506]
 gi|114537770|gb|EAU40894.1| tRNA pseudouridine synthase A [Fulvimarina pelagi HTCC2506]
          Length = 261

 Score =  258 bits (658), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 127/248 (51%), Positives = 170/248 (68%), Gaps = 2/248 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ Y GWQRQ +  S+Q  IE+A   + G   V+ GAGRTDSGVHA  Q
Sbjct: 1   MPRYKLTVEYDGTPYAGWQRQADEPSVQAVIEEAAHRLCGTNPVLFGAGRTDSGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL + +    +  ALNA+++  + + IL+   V   F ARFSA +R Y YRI  R+
Sbjct: 61  VAHIDLPKAYAGGTVRDALNAHMR-DEPVVILSAEEVGADFDARFSARKRWYRYRIFNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VNS 179
           AP A+ +G+ W + K LD E M  AAQ L G HDFTTFRS HCQA +PIRT++  + V +
Sbjct: 120 APAAILRGKVWWVSKLLDTEAMHEAAQVLAGTHDFTTFRSTHCQAKNPIRTLEKLEVVRA 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I I  +A+SFLH QIRSF G+LKLVG+G+WT+TD+ +AL+A+DR  CGP+APP GL
Sbjct: 180 NGEEIHIVAMAQSFLHNQIRSFAGTLKLVGEGRWTATDVSEALKAKDRTACGPVAPPYGL 239

Query: 240 YFDSVEYS 247
           Y  ++EY+
Sbjct: 240 YLTAIEYT 247


>gi|149185872|ref|ZP_01864187.1| tRNA pseudouridine synthase A [Erythrobacter sp. SD-21]
 gi|148830433|gb|EDL48869.1| tRNA pseudouridine synthase A [Erythrobacter sp. SD-21]
          Length = 249

 Score =  257 bits (656), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 124/246 (50%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IE++G+ +FG QRQ NG S+Q S+E+A F VTGE V +H AGRTD+GVHAL  
Sbjct: 1   MTRFALTIEFDGTPFFGLQRQDNGPSVQQSLEEAAFRVTGENVRLHSAGRTDTGVHALAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +H D+ ++  P  L +ALNA ++  D I++ +  +V   +HARFS   RSY+YRI  R+
Sbjct: 61  RSHMDIEKDIEPFRLMEALNAQVR-PDPIAVTHCGVVPDDWHARFSCTGRSYVYRIANRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL LE+ R W +P+ LD E M  AA+ LVG HDFTTFRS+ CQ+ SP++T+D  DV   
Sbjct: 120 APLTLERNRLWQVPQDLDHEAMDRAAKALVGLHDFTTFRSVQCQSQSPVKTLDRLDVERD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I   ARSFLH Q+RS VG L LVG G+W    L +AL+A+DR+  G  APP GLY
Sbjct: 180 GEEVRIHAAARSFLHHQVRSVVGCLALVGMGRWREEQLAEALEAKDRQALGLNAPPHGLY 239

Query: 241 FDSVEY 246
           F +  Y
Sbjct: 240 FVAATY 245


>gi|295691224|ref|YP_003594917.1| tRNA pseudouridine synthase A [Caulobacter segnis ATCC 21756]
 gi|295433127|gb|ADG12299.1| tRNA pseudouridine synthase A [Caulobacter segnis ATCC 21756]
          Length = 247

 Score =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 124/246 (50%), Positives = 165/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G  Y G+Q Q    S+QG+IE A+    G+ V +  AGRTD+GVHA  Q
Sbjct: 1   MPRYRLLVEYDGRPYAGFQAQATLPSVQGAIEAAVKAFCGQDVRIAAAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H DL ++W    +  ALNA+L   + +SIL+  + +  +HARFSA  R YLYRI+ R+
Sbjct: 61  VVHVDLEKDWPAQTVFNALNAHL-THEAVSILSAEVAEGDWHARFSANERRYLYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP AL+KGR W + K LD E M  AAQHLVG HDFTTFR +HCQ+ SP++T+D   V   
Sbjct: 120 APPALDKGRVWHMKKDLDAEAMHAAAQHLVGLHDFTTFRDMHCQSKSPVKTLDVARVRRV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +   ARSFLH Q+RS  G+L  VG G+WT  D++ AL+A+DR+ECGP+AP +GLY
Sbjct: 180 GEEIHLDFEARSFLHRQVRSMTGTLVEVGAGRWTPDDVKAALEAKDRRECGPVAPADGLY 239

Query: 241 FDSVEY 246
              V Y
Sbjct: 240 LVGVGY 245


>gi|307943162|ref|ZP_07658507.1| tRNA pseudouridine synthase A [Roseibium sp. TrichSKD4]
 gi|307773958|gb|EFO33174.1| tRNA pseudouridine synthase A [Roseibium sp. TrichSKD4]
          Length = 271

 Score =  256 bits (654), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 127/246 (51%), Positives = 162/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G  + GWQRQ NG S QG IE+AI   +GE V + GAGRTD+GVHAL Q
Sbjct: 1   MPRYKLTVEYDGRPFCGWQRQSNGPSAQGVIERAIKAFSGEDVTIGGAGRTDTGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL  +W    +  ALN + +  D + IL        F ARFSAIRRSY YRI  R 
Sbjct: 61  VAHADLSEDWPEKTVMGALNFHCQ-PDPVVILACEKKHDGFDARFSAIRRSYRYRIHNRL 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL  E G AW +   LD + M  AAQ  VG HDFTTFR   CQA SP++T+++F V   
Sbjct: 120 PPLTHELGLAWHVKHELDADAMNEAAQEFVGHHDFTTFRHSRCQAKSPVKTLENFTVRRE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +I     +RSFLH Q+RS VG+L+LVG+G+WT++D+ +AL A+DRK CGP+AP +GLY
Sbjct: 180 GEIILAECSSRSFLHNQVRSMVGTLRLVGEGRWTASDVGEALAARDRKACGPVAPADGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LTRVDY 245


>gi|87200906|ref|YP_498163.1| tRNA pseudouridine synthase A [Novosphingobium aromaticivorans DSM
           12444]
 gi|87136587|gb|ABD27329.1| tRNA pseudouridine synthase A [Novosphingobium aromaticivorans DSM
           12444]
          Length = 254

 Score =  256 bits (654), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 126/245 (51%), Positives = 169/245 (68%), Gaps = 1/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + +E+NG  Y G+QRQ +G S+Q ++E+A+  VTGE V ++ AGRTD+GVHAL   A
Sbjct: 7   RFALTLEWNGGPYMGFQRQSHGPSVQQAVEEAVHSVTGEAVALNAAGRTDTGVHALGMRA 66

Query: 63  HFDLVREWVPVILCKALNAYLKISD-TISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFDL R + P  + +ALNA L+++   +++L+   V   +HARFS   R+Y YRII R+A
Sbjct: 67  HFDLSRAFDPFRMMEALNARLRLAGHPVAVLDCIEVAPDWHARFSCTGRAYEYRIINRRA 126

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           PL L+ GRAW I K LD   M  AAQ LVG HDFTTFRS+HCQ++SP++T+D  DV   G
Sbjct: 127 PLTLDLGRAWRIAKPLDETVMHEAAQLLVGHHDFTTFRSVHCQSASPLKTLDRLDVRRDG 186

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + +   ARSFLH Q+RS VG L LVG G+W+   L +AL A+DR   G  APPEGLYF
Sbjct: 187 DRVIVEAAARSFLHHQVRSMVGCLALVGQGQWSVAQLGEALAAKDRSRLGLNAPPEGLYF 246

Query: 242 DSVEY 246
            S +Y
Sbjct: 247 VSAQY 251


>gi|23016535|ref|ZP_00056290.1| COG0101: Pseudouridylate synthase [Magnetospirillum magnetotacticum
           MS-1]
          Length = 256

 Score =  256 bits (654), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 123/246 (50%), Positives = 167/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G+ + GWQRQ  G S+QG +E+A+  +TG    ++ AGRTD+GVHA  Q
Sbjct: 1   MPRYRLLVEYDGTPFNGWQRQDKGLSVQGVLEQAVEKLTGSPCTINAAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R++    +  ALN ++K    ++++   +V   FHARFSA+ RSYLYRI+ R+
Sbjct: 61  VAHVDLPRDYPADTVRDALNYHMK-PKPVAVVAAELVGDDFHARFSAVGRSYLYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APLAL++ RAW +P SLD E M   A+ L+G HDFTTFR+  CQA SP++T+D  DV   
Sbjct: 120 APLALDQHRAWWVPVSLDAEAMAEGARRLLGHHDFTTFRASECQAKSPMKTLDVLDVTRV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I   ARSFLH Q+R+ VG+LKLVG+GKW+  D+ +AL A DR + GP AP  GL 
Sbjct: 180 GEEIRIIAEARSFLHHQVRNMVGTLKLVGEGKWSPDDMARALAACDRTKGGPTAPAAGLC 239

Query: 241 FDSVEY 246
              V Y
Sbjct: 240 LTGVSY 245


>gi|90422327|ref|YP_530697.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris BisB18]
 gi|123089809|sp|Q21B58|TRUA_RHOPB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|90104341|gb|ABD86378.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris BisB18]
          Length = 245

 Score =  256 bits (653), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 131/246 (53%), Positives = 172/246 (69%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +IIEY+G+ Y GWQ Q NG S+QG++E A+  + G+ V V+GAGRTD+GVHAL Q
Sbjct: 1   MPRYKLIIEYDGAPYCGWQIQDNGPSVQGALETAVKAICGKFVRVNGAGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ +E+ P  L   LNA+L+    I +L+  IV   F ARFSAI+R Y+YRI  R+
Sbjct: 61  VAHCDIAKEFAPGRLRDGLNAHLR-PHPIGVLSAEIVPDDFEARFSAIKRHYVYRISNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A LAL+ G+ W +P+ LD + M  AAQ LVG+HDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 ANLALQIGKVWRLPRRLDTDAMHAAAQRLVGKHDFTTFRDTECQAKSPDKTLDQLDVIRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARSFLH+Q+RS VGSL  VG+G+W++ DL  AL A+ R  CGP+APP+GLY
Sbjct: 180 GDNVSIITSARSFLHSQVRSMVGSLVWVGEGRWSADDLAAALAARRRTACGPVAPPDGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVKVDY 245


>gi|326388515|ref|ZP_08210109.1| tRNA pseudouridine synthase A [Novosphingobium nitrogenifigens DSM
           19370]
 gi|326206980|gb|EGD57803.1| tRNA pseudouridine synthase A [Novosphingobium nitrogenifigens DSM
           19370]
          Length = 261

 Score =  255 bits (652), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 126/246 (51%), Positives = 170/246 (69%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +E++G+ + G+QRQ +G S+Q ++E+A   V GE +V+H AGRTD+GVHA   
Sbjct: 1   MTRFALTLEWDGTPFMGFQRQAHGPSVQQAVEEATQSVIGEEIVLHAAGRTDTGVHARGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AH +L R++ P  L +A+NA LK    I++L+   V   +HARFS I R+Y YRII R+
Sbjct: 61  RAHLELSRDFDPFRLGEAINARLK-PHPIAVLDCVRVADDWHARFSCIGRAYEYRIINRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL LE GRAW + + LD E M  AAQ LVG HDFTTFRS+HCQA+SP++T+D  DV   
Sbjct: 120 APLTLEAGRAWRVTRPLDAEAMHEAAQVLVGHHDFTTFRSVHCQAASPLKTLDRLDVRRV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARSFLH Q+RS VG L LVG G+W   D+  AL+A++R + G  APPEGLY
Sbjct: 180 GDEVLIAAAARSFLHHQVRSMVGCLALVGLGQWNRDDMAAALEAKNRCKLGLNAPPEGLY 239

Query: 241 FDSVEY 246
           F S +Y
Sbjct: 240 FISAQY 245


>gi|328545265|ref|YP_004305374.1| tRNA pseudouridine synthase A [polymorphum gilvum SL003B-26A1]
 gi|326415007|gb|ADZ72070.1| tRNA pseudouridine synthase A [Polymorphum gilvum SL003B-26A1]
          Length = 276

 Score =  255 bits (652), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 121/246 (49%), Positives = 163/246 (66%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQRQ NG S+Q  IE+A+    GE V + GAGRTD+GVHA  Q
Sbjct: 1   MPRYKLTIEYDGRPFCGWQRQANGPSVQAVIERAVKAFCGEEVTIGGAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R+W    +  ALN + +  D +++L    +   F +RFSAIRR+Y YRI+ R 
Sbjct: 61  VAHVDLSRDWPADTVLGALNFHCQ-PDPVALLACEKMHAGFDSRFSAIRRAYRYRIVNRV 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL  E+G AW +   LD E M  AAQ  VG HDFTTFR   CQA SP++T++ F V   
Sbjct: 120 PPLTYERGLAWHVKPPLDAEAMHAAAQVFVGHHDFTTFRHARCQAKSPVKTLEFFAVRRE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++     +RSFLH Q+RS VG+L+LVG+G+W +  + +AL A++RK CGP+APP+GLY
Sbjct: 180 GDVVVAECASRSFLHNQVRSMVGTLRLVGEGRWDAQTVREALAARNRKACGPVAPPDGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LTRVDY 245


>gi|126462985|ref|YP_001044099.1| tRNA pseudouridine synthase A [Rhodobacter sphaeroides ATCC 17029]
 gi|166228755|sp|A3PLW1|TRUA_RHOS1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|126104649|gb|ABN77327.1| tRNA pseudouridine synthase A [Rhodobacter sphaeroides ATCC 17029]
          Length = 255

 Score =  255 bits (652), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 123/251 (49%), Positives = 164/251 (65%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQRQ   +S+QG+IE A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALRIEYDGGPFAGWQRQAAQASVQGAIETALGRLEPGPHTIAAAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DLVREW P  L  ALNA+LK    ++I+  + V ++FHARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDLVREWDPFRLAGALNAHLK-PLPVAIVAAARVPEEFHARFSAVERRYLFRLLARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   ++GR W +P  LD E MR  A HLVGRHDFTTFR+  CQA+SP++T+D   + + 
Sbjct: 120 APEVHDRGRVWRVPHPLDPEAMRAGAAHLVGRHDFTTFRAAGCQAASPVKTLDALTLETV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      + ARSFLH Q+RS VG+L+ VG G WT   + +AL+A DR  CGP+ PP
Sbjct: 180 EGMNGTEYRFHLRARSFLHNQVRSIVGTLERVGAGAWTPDQVREALEAHDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLTGVGYP 250


>gi|304392304|ref|ZP_07374245.1| tRNA pseudouridine synthase A [Ahrensia sp. R2A130]
 gi|303295408|gb|EFL89767.1| tRNA pseudouridine synthase A [Ahrensia sp. R2A130]
          Length = 251

 Score =  255 bits (651), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 129/251 (51%), Positives = 162/251 (64%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  IIEY+G  Y GWQRQ +  S+QG+IE A+  +     +V GAGRTD+GVHAL Q
Sbjct: 1   MGRYRFIIEYDGKPYAGWQRQPDQPSVQGAIEAALGRLGEPDPIVQGAGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL R W    L +ALNA+L K  D ++I++    D +FHARFSA +R+YLYRII  
Sbjct: 61  VAHSDLTRPWTGFRLAEALNAHLRKAGDPVAIIDCEPCDDEFHARFSATQRAYLYRIIDH 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF---D 176
           +APLA++ GRAW +   LD + M  AA  LVG HDFTTFRS  CQA SP++T+       
Sbjct: 121 RAPLAVDAGRAWNVKTPLDVDAMNKAAARLVGEHDFTTFRSTECQARSPVKTLGTLVATR 180

Query: 177 VNSFG-NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           V   G + +EI   ARS+LH Q+RS  G L+LVG GKW+  D   +L A DR  C P+AP
Sbjct: 181 VQRHGRSEVEITTTARSYLHNQVRSLAGCLRLVGCGKWSPDDAAASLAAMDRTACAPVAP 240

Query: 236 PEGLYFDSVEY 246
             GLY  SV Y
Sbjct: 241 AHGLYLTSVTY 251


>gi|77464142|ref|YP_353646.1| tRNA pseudouridine synthase A [Rhodobacter sphaeroides 2.4.1]
 gi|123591335|sp|Q3J0D9|TRUA_RHOS4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|77388560|gb|ABA79745.1| tRNA pseudouridine synthase [Rhodobacter sphaeroides 2.4.1]
          Length = 255

 Score =  255 bits (651), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 123/251 (49%), Positives = 165/251 (65%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQRQ   +S+QG+IE A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALRIEYDGGPFAGWQRQAAQASVQGAIETALGRLEPGPHTIAAAGRTDTGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DLVREW P  L  ALNA+LK    ++I+  + V ++FHARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDLVREWDPFRLAGALNAHLK-PLPVAIVAAARVPEEFHARFSAVERRYLFRLLARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   ++GR W +P  LD E MR  A HLVGRHDFTTFR+  CQA+SP++T+D   + + 
Sbjct: 120 APEVHDRGRVWRVPHPLDPEAMRAGAAHLVGRHDFTTFRAAGCQAASPVKTLDALTLETV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      + ARSFLH Q+RS VG+L+ VG G WT   + +AL A+DR  CGP++PP
Sbjct: 180 EGMNGTEYRFHLRARSFLHNQVRSIVGTLERVGAGAWTPDQVREALDARDRAACGPVSPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLTGVGYP 250


>gi|315497922|ref|YP_004086726.1| tRNA pseudouridine synthase a [Asticcacaulis excentricus CB 48]
 gi|315415934|gb|ADU12575.1| tRNA pseudouridine synthase A [Asticcacaulis excentricus CB 48]
          Length = 257

 Score =  254 bits (650), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 124/246 (50%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  ++EY+G  Y G+Q Q N  ++QGS+E+AI   +GE + +  AGRTD+GVHA  Q
Sbjct: 1   MPRYSCLVEYDGRPYKGFQAQDNLPTVQGSLERAILGFSGETLRITAAGRTDTGVHASGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FDL + + P ++  A+NAYL I + I++   +IVD  F ARFSA  R YLYRI+ R+
Sbjct: 61  VITFDLPKTYRPDVVRDAMNAYL-IPEPIAVREAAIVDDDFSARFSATGRMYLYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP ALE+GR W + K LD E M  AAQHL+GRHDFTTFR   CQA+SPI+T+D   V   
Sbjct: 120 APPALEQGRVWHVKKPLDAEVMADAAQHLIGRHDFTTFRDTECQAASPIKTLDIARVKRV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +   +RSFLH Q+RS  G+L   G G+WT+ D++ AL+A+DR+ CG +APPEGL 
Sbjct: 180 GEEIHLVFASRSFLHRQVRSMTGTLVEAGIGRWTAADVKAALEARDRRACGQVAPPEGLC 239

Query: 241 FDSVEY 246
              V +
Sbjct: 240 LTHVTF 245


>gi|103485743|ref|YP_615304.1| tRNA pseudouridine synthase A [Sphingopyxis alaskensis RB2256]
 gi|123253621|sp|Q1GWK1|TRUA_SPHAL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|98975820|gb|ABF51971.1| tRNA pseudouridine synthase A [Sphingopyxis alaskensis RB2256]
          Length = 246

 Score =  254 bits (649), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 124/246 (50%), Positives = 164/246 (66%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IEY+G  Y GWQRQ +G S+Q +IE+AI   T E V V  AGRTD+GVHA+  
Sbjct: 1   MTRFALTIEYDGRPYMGWQRQAHGPSVQQAIEEAIHRFTAEEVQVLSAGRTDAGVHAIAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AH D+ +   P  L +ALNA L+ +  I+++   +V   +HARF+ I RSY YRI+ R+
Sbjct: 61  RAHVDIEKPLTPFKLTEALNAQLRPA-PIAVIGCEVVPDDWHARFACIGRSYEYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL  +KG AW + + LD + M  AAQ L+G HDFTTFRS HCQ+ SP++T+D   V+  
Sbjct: 120 APLTWDKGLAWQVARPLDVDAMHEAAQQLIGLHDFTTFRSAHCQSQSPVKTLDRLTVSRH 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I   ARSFLH Q+RS VGSL LVG GKW++ DL+ AL+A DR+  G  APP+GLY
Sbjct: 180 GEEVIIEAAARSFLHHQVRSMVGSLALVGHGKWSARDLKAALEAADRQALGLNAPPDGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FVGAVY 245


>gi|16124533|ref|NP_419097.1| tRNA pseudouridine synthase A [Caulobacter crescentus CB15]
 gi|221233219|ref|YP_002515655.1| tRNA pseudouridine synthase A [Caulobacter crescentus NA1000]
 gi|42559871|sp|Q9ABF0|TRUA_CAUCR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254789610|sp|B8GYF0|TRUA_CAUCN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|13421415|gb|AAK22265.1| tRNA pseudouridine synthase [Caulobacter crescentus CB15]
 gi|220962391|gb|ACL93747.1| tRNA pseudouridine synthase A [Caulobacter crescentus NA1000]
          Length = 247

 Score =  254 bits (648), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 123/246 (50%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G  Y G+Q Q    S+QG+IE A+    G+ V +  AGRTD+GVHA  Q
Sbjct: 1   MPRYRLLVEYDGRPYAGFQAQATLPSVQGAIEAAVKAFCGQEVRIAAAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H DL ++W    +  ALNA+L   + +SIL+  + ++ +HARFSA  R YLYRI+ R+
Sbjct: 61  VVHVDLDKDWPAQTVFNALNAHL-TREAVSILSAEVAEEGWHARFSANERRYLYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP AL+KGR W + K LD E M  AAQHL+G HDFTTFR +HCQ+ SP++T+D   V   
Sbjct: 120 APPALDKGRVWHMKKDLDHEAMHAAAQHLIGLHDFTTFRDMHCQSKSPVKTLDVARVRRV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I +   ARSFLH Q+RS  G+L  VG G+WT  D++ AL+A+DR+ECGP+AP +GLY
Sbjct: 180 GEEIHLDFEARSFLHRQVRSMTGTLVEVGAGRWTVDDVKAALEARDRRECGPVAPADGLY 239

Query: 241 FDSVEY 246
              V Y
Sbjct: 240 LVGVGY 245


>gi|254473752|ref|ZP_05087147.1| tRNA pseudouridine synthase A [Pseudovibrio sp. JE062]
 gi|211957138|gb|EEA92343.1| tRNA pseudouridine synthase A [Pseudovibrio sp. JE062]
          Length = 302

 Score =  253 bits (647), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 126/246 (51%), Positives = 161/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + I+Y+G  + GWQRQ NG ++QG IE+AI   TGE V + GAGRTDSGVHA  Q
Sbjct: 27  MPRYKITIDYDGRPFVGWQRQDNGPTVQGVIERAIKSFTGETVTIGGAGRTDSGVHATGQ 86

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W    +  ALN + +  D ++IL+       F ARFSAIRR Y Y+I  R 
Sbjct: 87  VAHLDLSKDWPAETVKNALNFHAQ-PDPVAILDCEKAGLGFDARFSAIRRHYRYKIANRL 145

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL  ++G AW +   LD E M  AAQ L+G HDFTTFR   CQA SP +T++   V   
Sbjct: 146 EPLTHDRGLAWYVKPELDAEAMNEAAQVLLGHHDFTTFRHTRCQAKSPWKTMERICVYRQ 205

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + +   +RSFLH Q+RS VGSL+LVG+G+WT  DL+ AL+A DRK CGP+A PEGLY
Sbjct: 206 GYHVFLECSSRSFLHNQVRSMVGSLRLVGEGRWTKDDLKAALEACDRKACGPVAVPEGLY 265

Query: 241 FDSVEY 246
              V+Y
Sbjct: 266 LTQVDY 271


>gi|221640010|ref|YP_002526272.1| tRNA pseudouridine synthase A [Rhodobacter sphaeroides KD131]
 gi|254764862|sp|B9KKX4|TRUA_RHOSK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|221160791|gb|ACM01771.1| tRNA pseudouridine synthase A [Rhodobacter sphaeroides KD131]
          Length = 255

 Score =  253 bits (646), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 125/251 (49%), Positives = 165/251 (65%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQRQ   +S+QG+IE A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALRIEYDGGPFAGWQRQAAQASVQGAIETALGRLELGPHTIAAAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL REW P  L  ALNA+LK    ++I+  + V ++FHARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDLAREWDPFRLAGALNAHLK-PLPVAIVAAARVSEEFHARFSAVERRYLFRLLARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   ++GR W +P  LD E MR  A HLVGRHDFTTFR+  CQA+SPI+T+D   + + 
Sbjct: 120 APEVHDRGRVWRVPHPLDAEAMRAGAAHLVGRHDFTTFRAAGCQAASPIKTLDALTLETV 179

Query: 181 --GNLIEIR--VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              N  E R  + ARSFLH Q+RS VG+L+ VG G WT   + +AL A+DR  CGP+ PP
Sbjct: 180 EGANGTEYRFHLRARSFLHNQVRSIVGTLERVGAGAWTPDQVREALDARDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLTGVGYP 250


>gi|167648522|ref|YP_001686185.1| tRNA pseudouridine synthase A [Caulobacter sp. K31]
 gi|189029993|sp|B0T1S6|TRUA_CAUSK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|167350952|gb|ABZ73687.1| tRNA pseudouridine synthase A [Caulobacter sp. K31]
          Length = 249

 Score =  253 bits (646), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 121/246 (49%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  Y G+Q Q +  S+QG+IE A+   TG+ + +  AGRTD+GVHA  Q
Sbjct: 1   MPRYRLTIEYDGRPYNGFQAQASQPSVQGAIEAAVKAFTGQTIRIAAAGRTDTGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H DL R+W    +  ALNA+L + + IS+L+  +V   +HARFSA  R YLYRI+ R+
Sbjct: 61  VVHVDLERDWPAETVMNALNAHL-VREAISVLDAVVVSDDWHARFSANERRYLYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP ALE+G+ W + K +D + M+ AAQ LVG HDFTTFR + CQA SP++T+D   V+  
Sbjct: 120 APPALERGKVWHVKKPIDADAMQTAAQALVGLHDFTTFRDMACQAKSPLKTLDVARVSRV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + +   ARSFLH Q+RS  G+L  VG G+WT+ D+  AL+A+DR  CGP+AP +GLY
Sbjct: 180 GDEVHLVFEARSFLHRQVRSMTGTLAEVGVGRWTADDVMAALEARDRTACGPVAPADGLY 239

Query: 241 FDSVEY 246
              V Y
Sbjct: 240 LTGVGY 245


>gi|332559018|ref|ZP_08413340.1| tRNA pseudouridine synthase A [Rhodobacter sphaeroides WS8N]
 gi|332276730|gb|EGJ22045.1| tRNA pseudouridine synthase A [Rhodobacter sphaeroides WS8N]
          Length = 255

 Score =  253 bits (645), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 122/251 (48%), Positives = 163/251 (64%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQRQ   +S+QG+IE A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALRIEYDGGPFAGWQRQAAQASVQGAIETALGRLEPGPHTIAAAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R+W P  L  ALNA+LK    ++I+  + V ++FHARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDLARDWDPFRLAGALNAHLK-PLPVAIVAAARVPEEFHARFSAVERRYLFRLLARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   ++GR W +P  LD E MR  A HLVGRHDFTTFR+  CQA+SPI+T+D   + + 
Sbjct: 120 APEVHDRGRVWRVPHPLDAEAMRAGAAHLVGRHDFTTFRAAGCQAASPIKTLDALTLETV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      + ARSFLH Q+RS VG+L+ VG G WT   + +AL A+DR  CGP+ PP
Sbjct: 180 EGMNGTEYRFHLRARSFLHNQVRSIVGTLERVGAGAWTPDQVREALDARDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLTGVGYP 250


>gi|115522681|ref|YP_779592.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris BisA53]
 gi|122297686|sp|Q07TX2|TRUA_RHOP5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|115516628|gb|ABJ04612.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris BisA53]
          Length = 246

 Score =  253 bits (645), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 132/247 (53%), Positives = 169/247 (68%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +IIEY+G+ Y GWQ Q+NG SIQG++E A   + GE + V GAGRTD+GVHAL Q
Sbjct: 1   MPRYKLIIEYDGTPYCGWQIQENGPSIQGALEDAAKAICGEAIRVRGAGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ ++  P  L  ALNA+L+    I ++   IV   F ARFSAI+R Y+YRI  R+
Sbjct: 61  VAHCDVPKQLPPGRLRDALNAHLR-PQPIGVITAEIVPDDFEARFSAIKRHYVYRISNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A LAL   RAW +P+ LD + M  AAQ L+G+HDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 ANLALAINRAWRVPRRLDSDAMHEAAQRLIGKHDFTTFRDTECQAKSPDKTLDQLDVIRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I   ARSFLH+Q+RS VGSL  VG+G+W++ DL  AL A+ R  CGP+APP+GLY
Sbjct: 180 GDEIRIVTSARSFLHSQVRSMVGSLVWVGEGRWSADDLAAALAARSRSACGPVAPPDGLY 239

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 240 LVKVDYE 246


>gi|294012442|ref|YP_003545902.1| tRNA pseudouridine synthase A [Sphingobium japonicum UT26S]
 gi|292675772|dbj|BAI97290.1| tRNA pseudouridine synthase A [Sphingobium japonicum UT26S]
          Length = 248

 Score =  252 bits (644), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 128/246 (52%), Positives = 165/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+   +E++G  + GWQRQ +G S+Q ++E AIF VTGE V VH AGRTD+GVH L  
Sbjct: 1   MARFAFTVEFDGRPFMGWQRQAHGPSVQQAMEDAIFSVTGERVAVHAAGRTDAGVHGLGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AH D+ ++  P  L +ALNA L+ +  ++IL    V   +HARFS   RSY+YRI+ R+
Sbjct: 61  RAHADIAKDMTPFRLMEALNARLRPA-PVAILACETVPDDWHARFSCTGRSYVYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL  E G AW + + LD E M+ AAQ LVGRHDFTTFRS+HCQA SP++T+D  DV   
Sbjct: 120 APLTWESGLAWRVIQPLDAEAMQRAAQLLVGRHDFTTFRSVHCQAESPVKTLDRLDVERA 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARSFLH Q+RS VG L +VG G+W+  DLE A  A+DR   G  APP+GLY
Sbjct: 180 GDRLAIHAEARSFLHHQVRSMVGCLVMVGMGRWSVGDLEAARDAKDRAALGLNAPPDGLY 239

Query: 241 FDSVEY 246
           F S  Y
Sbjct: 240 FVSAHY 245


>gi|83951133|ref|ZP_00959866.1| tRNA pseudouridine synthase A [Roseovarius nubinhibens ISM]
 gi|83839032|gb|EAP78328.1| tRNA pseudouridine synthase A [Roseovarius nubinhibens ISM]
          Length = 258

 Score =  251 bits (642), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 122/250 (48%), Positives = 171/250 (68%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVHAL Q
Sbjct: 1   MPRYALKVEYHGAPFAGWQRQKDQPSVQGAIEAALSALEPGAHTIAAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R+W P  L +ALN +LK +  ++I   + V + +HARFSA+ R YL+R++TR+
Sbjct: 61  VAHCDLRRDWDPFRLSEALNYHLKPA-PVAITACAPVAEDWHARFSALERRYLFRLLTRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G  W IP  LD + M+ A +HLVGRHDFTTFRS  CQA+SP++T+D   +   
Sbjct: 120 APATHDAGLVWQIPHRLDTDAMQTACRHLVGRHDFTTFRSSICQAASPVKTLDELTITEH 179

Query: 181 GNLI--EIR--VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             +   E+R  + ARSFLH Q+RSFVG+L+ VG G+W+  D++ AL A++R  CGP++PP
Sbjct: 180 EGVSGWEVRFFLRARSFLHNQVRSFVGTLERVGAGRWSPDDVKAALDARNRAACGPVSPP 239

Query: 237 EGLYFDSVEY 246
            GLY   VEY
Sbjct: 240 HGLYLAGVEY 249


>gi|300024227|ref|YP_003756838.1| tRNA pseudouridine synthase A [Hyphomicrobium denitrificans ATCC
           51888]
 gi|299526048|gb|ADJ24517.1| tRNA pseudouridine synthase A [Hyphomicrobium denitrificans ATCC
           51888]
          Length = 246

 Score =  251 bits (640), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 132/247 (53%), Positives = 171/247 (69%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQ  G SIQG++E AI   +GE   V GAGRTD+GVHAL Q
Sbjct: 1   MPRYRITIEYDGTPFIGWQRQAEGVSIQGALETAIRKFSGEAPGVRGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL + W P  +  A+N +L+  + I ++  + VD  F ARFSA++R Y YR++TR+
Sbjct: 61  VAHFDLEKTWEPGRIRDAMNFHLR-PNPIGVVAAAQVDDAFDARFSAVKRYYEYRLLTRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP  L++ R W   ++LD   M  AAQ LVG+HDFTTFR+  CQA SP++T+D FDV+  
Sbjct: 120 APPILQRHRVWWTMQNLDAAAMHAAAQELVGKHDFTTFRAAQCQAKSPVKTLDVFDVSRE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I  RV ARSFLH Q+RS VGSLKLVG+GKW+  DL  AL A +R+ CGP+AP  GLY
Sbjct: 180 GEEIVCRVSARSFLHHQVRSMVGSLKLVGEGKWSRADLASALAAANREACGPVAPAAGLY 239

Query: 241 FDSVEYS 247
              V+Y 
Sbjct: 240 LVGVDYE 246


>gi|144900443|emb|CAM77307.1| Pseudouridylate synthase [Magnetospirillum gryphiswaldense MSR-1]
          Length = 245

 Score =  251 bits (640), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 125/246 (50%), Positives = 164/246 (66%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ ++IEY+G+ + GWQRQ NG S+QG +E AIF   G    V  AGRTD+GVHA  Q
Sbjct: 1   MPRFKLLIEYHGTPFVGWQRQDNGISVQGEVEAAIFRFCGLETTVTAAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFDL R+     +  ALN +LK    I++  + IV   FHARFSA+ RSYLYRI+ R+
Sbjct: 61  VIHFDLDRDVSAERVQGALNYHLK-PHPIAVRAVEIVPDDFHARFSALGRSYLYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP+A+E+ R W +   L+ E M+ AAQHL+GRHDFT+FR+  CQA SP +T+D   V   
Sbjct: 120 APVAIERERVWWVSVPLNAEAMQEAAQHLLGRHDFTSFRAAACQAQSPDKTLDLLQVTRT 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I +   ARSFLH Q+R+ VG+LKLVG+GKW    ++ AL+A+DR   GP APP+GLY
Sbjct: 180 DEEIRMIAEARSFLHHQVRNMVGTLKLVGEGKWHPDRVKAALEARDRAAAGPTAPPDGLY 239

Query: 241 FDSVEY 246
              V Y
Sbjct: 240 LTGVVY 245


>gi|83859280|ref|ZP_00952801.1| tRNA pseudouridine synthase A [Oceanicaulis alexandrii HTCC2633]
 gi|83852727|gb|EAP90580.1| tRNA pseudouridine synthase A [Oceanicaulis alexandrii HTCC2633]
          Length = 253

 Score =  250 bits (639), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 126/246 (51%), Positives = 159/246 (64%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G  + GWQRQ NG S+QG++E A   + G    V+GAGRTDSGVHAL Q
Sbjct: 1   MPRYKLTIEYDGGPFVGWQRQDNGPSVQGALEAAAAKLDGGPREVYGAGRTDSGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++     +  A+N +LK    I+++    V  +FHARF A RR Y+YR+  R+
Sbjct: 61  VAHVDLEKDLPADKVRDAINHHLK-PHPIAVVEAVRVTDEFHARFKAHRRGYIYRLHARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL L +G+ W + + LD E M  AAQHLVG HDFTTFR   CQA SP++++D   V   
Sbjct: 120 APLTLTRGQVWRVYQPLDVEAMHTAAQHLVGTHDFTTFRDSQCQADSPVKSLDKIAVFHS 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + V A SFLH Q+RS VGSL  VG GKWT  D + AL A DR  CGP+APP+GLY
Sbjct: 180 GEEIHVTVEAISFLHRQVRSIVGSLVEVGLGKWTPEDFKAALDAADRSRCGPVAPPDGLY 239

Query: 241 FDSVEY 246
              V Y
Sbjct: 240 LSLVAY 245


>gi|110679351|ref|YP_682358.1| tRNA pseudouridine synthase A [Roseobacter denitrificans OCh 114]
 gi|122972811|sp|Q168C1|TRUA_ROSDO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|109455467|gb|ABG31672.1| tRNA pseudouridine synthase A [Roseobacter denitrificans OCh 114]
          Length = 260

 Score =  250 bits (638), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 125/250 (50%), Positives = 165/250 (66%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EYNG+ + GWQRQK   +IQG+IE+A+  +      +  AGRTD+GVHA+ Q
Sbjct: 1   MHRYALKVEYNGAPFVGWQRQKEHPTIQGAIERALGKIAPGPHTIAAAGRTDAGVHAIAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R+W P  L +ALN +LK +  I+I   + VD ++HARFSA +R YL+RI+ R+
Sbjct: 61  VAHCDLERDWDPFRLSEALNYHLKPA-PIAITACTAVDAEWHARFSARQRQYLFRILCRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   +KG  W + + LD   MR AA  L+G+HDFTTFRS  CQA SP++T+D  DVN  
Sbjct: 120 APATHQKGLVWQVKQKLDVTAMREAAALLIGQHDFTTFRSTICQAESPVKTLDRLDVNEV 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              +G  I   V ARSFLH Q+RSFVG+L+ VG G  T  D+ +AL  +DR  CGP+ PP
Sbjct: 180 DTPYGREIHFDVRARSFLHNQVRSFVGTLERVGAGSSTPQDVARALALRDRAACGPVCPP 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLAHVVY 249


>gi|163733492|ref|ZP_02140935.1| tRNA pseudouridine synthase A [Roseobacter litoralis Och 149]
 gi|161393280|gb|EDQ17606.1| tRNA pseudouridine synthase A [Roseobacter litoralis Och 149]
          Length = 256

 Score =  248 bits (634), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 123/250 (49%), Positives = 168/250 (67%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ + GWQRQK  S++QG+IE+A+  +      +  AGRTD+GVHA+ Q
Sbjct: 1   MHRYALKVEYHGAPFVGWQRQKEHSTVQGAIEQALGKIAPAPHTIAAAGRTDAGVHAIAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DLVR+W P  L +ALN +LK +  I+I   ++VD  +HARFSA +R YL+RI+ R+
Sbjct: 61  VAHCDLVRDWDPFRLSEALNYHLKPA-PIAITACTVVDADWHARFSARQRQYLFRILCRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   ++G  W + ++LD   MR AA  L+G+HDFTTFRS  CQA SP++T+D  DV+  
Sbjct: 120 APATHQRGLVWQVKQNLDVAAMREAAALLIGQHDFTTFRSTICQAESPVKTLDRLDVSEV 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              +G  I   V ARSFLH Q+RSFVG+L+ VG G  T  D+ +AL  +DR  CGP+ PP
Sbjct: 180 ETPYGREIHFDVRARSFLHNQVRSFVGTLERVGAGSSTPQDVARALALRDRAACGPVCPP 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 YGLYLAHVVY 249


>gi|316932092|ref|YP_004107074.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris DX-1]
 gi|315599806|gb|ADU42341.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris DX-1]
          Length = 245

 Score =  248 bits (633), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 126/246 (51%), Positives = 169/246 (68%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q    S+QG++E A     GE V VHGAGRTD+GVHAL Q
Sbjct: 1   MPRYKLTIEYDGAPFCGWQLQPKLPSVQGALEAAALATCGEAVRVHGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH ++ + +    L  ALNA+L+  + +++L   IV + F ARFSA+RR Y YRI  R+
Sbjct: 61  VAHVEIAKPFRADKLRDALNAHLR-PNPVAVLAAEIVPETFEARFSAVRRHYRYRIANRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           + LAL+ G+ W +PK LD + M  AAQ L+G+HDFTTFR   CQA+SP +T+D  DV   
Sbjct: 120 SNLALDIGKVWRVPKPLDSDAMHRAAQVLIGKHDFTTFRDTECQAASPEKTLDVLDVIRN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ ++I   ARS+LH+Q+RS VGSL  VG+G+WT+ DL  AL A+ R  CGP+APPEGLY
Sbjct: 180 GDAVDIVTNARSYLHSQVRSMVGSLVWVGEGRWTADDLAAALAARKRSACGPVAPPEGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVQVDY 245


>gi|254460774|ref|ZP_05074190.1| tRNA pseudouridine synthase A [Rhodobacterales bacterium HTCC2083]
 gi|206677363|gb|EDZ41850.1| tRNA pseudouridine synthase A [Rhodobacteraceae bacterium HTCC2083]
          Length = 259

 Score =  248 bits (633), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 124/250 (49%), Positives = 159/250 (63%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ + GWQRQK   S+QG IE A+  +      +  AGRTDSGVHA  Q
Sbjct: 1   MPRYALKVEYHGAPFVGWQRQKTHVSVQGQIEAALAKLEPGNHTIGAAGRTDSGVHAWGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W P  L  ALN +LK  D ISI+  + V+  +HARFSA+ R Y +R++ R+
Sbjct: 61  VAHCDLAKDWDPFKLSGALNYHLK-PDPISIVACAEVNDDWHARFSALERRYEFRLLMRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   + G  W +P  LD   M+  AQHL+G HDFTTFRS  CQA SP++T+D   V   
Sbjct: 120 PPATHDAGLVWQVPHLLDVNAMQAGAQHLLGLHDFTTFRSSICQAQSPLKTLDELKVRQI 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I   V ARSFLH Q+RSFVG+L  VG G WT  D++ ALQAQDR+ CGP++PP
Sbjct: 180 DGPSGPEIRFTVRARSFLHNQVRSFVGTLGSVGSGAWTPDDVKSALQAQDRQACGPVSPP 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLAHVTY 249


>gi|197103844|ref|YP_002129221.1| tRNA pseudouridine synthase [Phenylobacterium zucineum HLK1]
 gi|196477264|gb|ACG76792.1| tRNA pseudouridine synthase [Phenylobacterium zucineum HLK1]
          Length = 246

 Score =  248 bits (632), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 121/246 (49%), Positives = 162/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY+G  + G+Q Q    +IQG+IE+A+    GE + +  AGRTD+GVHA  Q
Sbjct: 2   MPRYRLLIEYDGRPFNGFQAQDGLPTIQGAIERAVKAFCGEDLRLQAAGRTDTGVHARGQ 61

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H DL ++W    +  ALNA+L +   I++L  S+  + +HARFSA  R YLYRI+ R 
Sbjct: 62  VVHVDLAKDWPAETVRNALNAHL-VPQPIAVLEASVAPEGWHARFSAKERRYLYRILNRM 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP AL++GR W + K LD E M  AAQ LVG HDFTTFR + CQA SP++T+D   V   
Sbjct: 121 APPALDQGRVWHVKKPLDAEAMHEAAQALVGHHDFTTFRDLGCQAKSPMKTLDLASVRRE 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + +   +RSFLH Q+RS  G+L  VG G+WT  DL  AL+A+DR+ CGP+AP EGLY
Sbjct: 181 GDEVLLEFASRSFLHRQVRSMTGTLAEVGVGRWTRADLVAALEARDRRACGPVAPAEGLY 240

Query: 241 FDSVEY 246
              V Y
Sbjct: 241 LTGVAY 246


>gi|89055953|ref|YP_511404.1| tRNA pseudouridine synthase A [Jannaschia sp. CCS1]
 gi|123400973|sp|Q28LN3|TRUA_JANSC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|88865502|gb|ABD56379.1| tRNA pseudouridine synthase A [Jannaschia sp. CCS1]
          Length = 261

 Score =  247 bits (630), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 121/251 (48%), Positives = 161/251 (64%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY   IEY+G  + GWQRQ +  S+QG++E A+  +  ++  +  AGRTD+GVHAL Q
Sbjct: 1   MPRYAFRIEYDGHPFKGWQRQTDLPSVQGAVEAALAKLEADVPTIAAAGRTDTGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ R+W P  L +ALN +LK +  ++I   +     FHARFSA  RSY YR+I R+
Sbjct: 61  VAHADMQRDWDPFRLAEALNYHLKPA-PVAITACARAHDDFHARFSATWRSYTYRMICRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL   +G AW +  +LD   M   A+HL+G+HDFTTFR+ HCQA SPI+T+D   V   
Sbjct: 120 APLVHARGHAWAVRGTLDVTAMAEGARHLIGKHDFTTFRATHCQALSPIKTMDEIRVEEV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I   + A+SFLH Q+RS VGSL+ VG G W   D+ +AL+A DR ECG +APP
Sbjct: 180 SLPAGTEIRFHLKAQSFLHNQVRSIVGSLEHVGSGAWAPDDMRRALEACDRAECGTVAPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 DGLYMTGVGYD 250


>gi|86747801|ref|YP_484297.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris HaA2]
 gi|123293209|sp|Q2J2C4|TRUA_RHOP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|86570829|gb|ABD05386.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris HaA2]
          Length = 245

 Score =  246 bits (627), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 127/246 (51%), Positives = 169/246 (68%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q    S+QG++E A     GE V VHGAGRTD+GVHAL Q
Sbjct: 1   MPRYKLTIEYDGAPFCGWQLQPTLPSVQGALEAAALATCGEAVRVHGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + +    L  ALNA+++    I++L+  +V   F ARFSAIRR Y YRI+ R+
Sbjct: 61  VAHVDIPKPFRADKLRDALNAHVR-PHPIAVLSAELVADDFEARFSAIRRHYRYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           + LALE G+ W +PK LD + M  AAQ L+G+HDFTTFR   CQA+SP +T+D  DV   
Sbjct: 120 SNLALELGKVWRVPKPLDTDAMHRAAQVLIGKHDFTTFRDTECQAASPAKTLDVLDVVRN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ ++I   ARS+LH+Q+RS VGSL  VG+G+WT+ DL  AL A+ R  CGP+APP+GLY
Sbjct: 180 GDAVDIITNARSYLHSQVRSMVGSLVWVGEGRWTADDLAAALAARRRSACGPVAPPDGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVQVDY 245


>gi|254510182|ref|ZP_05122249.1| tRNA pseudouridine synthase A [Rhodobacteraceae bacterium KLH11]
 gi|221533893|gb|EEE36881.1| tRNA pseudouridine synthase A [Rhodobacteraceae bacterium KLH11]
          Length = 255

 Score =  245 bits (626), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 121/250 (48%), Positives = 162/250 (64%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G  + GWQRQK   S+QG+IE A+  +      +  AGRTD+GVHAL Q
Sbjct: 1   MPRYALKVEYHGEPFAGWQRQKEQPSVQGAIEAALSRIEPGDHTIAAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W P  L +ALN +LK    ++I+  + V+  +HARFSA+ R YL+RI+ R+
Sbjct: 61  VAHCDLTKDWDPFRLSEALNYHLK-PQPVAIVKAARVNDDWHARFSALERQYLFRILMRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   +KG+ W I  +LD   M+  A  L+G+HDFTTFRS  CQA+SP++T+D   V   
Sbjct: 120 APATHDKGQVWQINHTLDVAAMQAGADMLIGQHDFTTFRSSICQAASPVKTLDALRVEQV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I   V ARSFLH Q+RSFVG+L+ VG G WT  D+  AL+A DR  CGP+ PP
Sbjct: 180 QGFSGAEIHFHVRARSFLHNQVRSFVGTLERVGAGAWTPEDVRDALEAADRAACGPVCPP 239

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 240 QGLYLARVGY 249


>gi|126736576|ref|ZP_01752316.1| tRNA pseudouridine synthase A [Roseobacter sp. CCS2]
 gi|126713889|gb|EBA10760.1| tRNA pseudouridine synthase A [Roseobacter sp. CCS2]
          Length = 255

 Score =  245 bits (626), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 118/250 (47%), Positives = 167/250 (66%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G+ + GWQRQ +  S+QG+IE A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALLVEYHGAPFAGWQRQNDQPSVQGAIEAALAKLEPRDHTIAAAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ R+W P  L +ALN +LK +  ++I+N + V   +HARF A+ R YL+R+++R+
Sbjct: 61  VAHCDMERDWDPFRLSEALNFHLKPA-PVAIVNCAQVADDWHARFDAVERQYLFRLMSRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL  + G+ W +   LD + M+  A  L+G+HDFTTFRS  CQA SP++T+D   V + 
Sbjct: 120 APLTSDAGQMWRVKHPLDADAMQAGADQLLGQHDFTTFRSSICQAKSPVKTLDALRVEAL 179

Query: 181 --GNLIEIR--VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              N  E R  V ARSFLH Q+RSFVG+L+ VG   WT  D+ KAL A+DR  CGP+ PP
Sbjct: 180 PHANGTEYRFHVRARSFLHNQVRSFVGTLERVGAEAWTPDDVGKALAAKDRSACGPVCPP 239

Query: 237 EGLYFDSVEY 246
           +GLY  +V+Y
Sbjct: 240 QGLYLAAVKY 249


>gi|83943967|ref|ZP_00956424.1| tRNA pseudouridine synthase A [Sulfitobacter sp. EE-36]
 gi|83954540|ref|ZP_00963251.1| tRNA pseudouridine synthase A [Sulfitobacter sp. NAS-14.1]
 gi|83840824|gb|EAP79995.1| tRNA pseudouridine synthase A [Sulfitobacter sp. NAS-14.1]
 gi|83845214|gb|EAP83094.1| tRNA pseudouridine synthase A [Sulfitobacter sp. EE-36]
          Length = 262

 Score =  245 bits (626), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 119/251 (47%), Positives = 168/251 (66%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQ + +S+QG+IE A+  +      +  AGRTD+GVHAL Q
Sbjct: 1   MQRYALKIEYHGAPFVGWQRQIDLASVQGAIEDALAKIEPRAHNIAAAGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ R+W P  L +A+N +LK    I+I++   VD  FHARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDMERDWTPFRLSEAINYHLK-PLPIAIVDCVAVDDDFHARFSALERRYLFRVLVRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
            P   + G  W + K LD + MR AA HL+G HDFTTFRS  CQA +P++T+D  D+  +
Sbjct: 120 PPATHQAGLVWQVKKPLDIDRMREAATHLIGEHDFTTFRSTICQAQTPVKTLDRVDMTEH 179

Query: 179 SFGNLIEIR--VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             G  +E++  V ARSFLH Q+RS VG+L+ VG G +   D+++ L A+DR+ CGP+APP
Sbjct: 180 PVGGGVEVQFDVRARSFLHNQVRSIVGTLERVGAGSFAPDDVKQMLAARDRQACGPVAPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLSHVTYE 250


>gi|84515131|ref|ZP_01002494.1| tRNA pseudouridine synthase A [Loktanella vestfoldensis SKA53]
 gi|84511290|gb|EAQ07744.1| tRNA pseudouridine synthase A [Loktanella vestfoldensis SKA53]
          Length = 257

 Score =  244 bits (624), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 118/251 (47%), Positives = 160/251 (63%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G+ + GWQRQ    S+QG+IE A+  ++     +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALLVEYHGAPFAGWQRQTGLPSVQGAIEAALAKLSPGPHTIAAAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL  +W P  L +ALN +LK  D ++IL  ++V   +HARF A+ R YL+R+I R+
Sbjct: 61  VAHCDLPGDWDPFRLSEALNYHLK-PDPVAILGCALVADDWHARFDAVERQYLFRVIARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           APL  E G+ W +   LD   M+  A HL+G HDFTTFRS  CQA SP++T+D   +   
Sbjct: 120 APLTSEAGQMWRVNHDLDAAAMQAGADHLLGLHDFTTFRSSICQAKSPVKTLDELRIEVV 179

Query: 179 --SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             + G      V ARSFLH Q+RSFVG+L+ VG G W   D+ +AL A+DR  CGP+ PP
Sbjct: 180 QRAIGTEYRFHVRARSFLHNQVRSFVGTLERVGAGAWQPGDVARALTARDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLAGVRYP 250


>gi|307294617|ref|ZP_07574459.1| tRNA pseudouridine synthase A [Sphingobium chlorophenolicum L-1]
 gi|306879091|gb|EFN10309.1| tRNA pseudouridine synthase A [Sphingobium chlorophenolicum L-1]
          Length = 248

 Score =  244 bits (623), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 125/246 (50%), Positives = 161/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+   +E++G  + GWQRQ +G S+Q +IE AIF V+GE  V+H AGRTD+GVH +  
Sbjct: 1   MTRFAFTVEFDGRPFMGWQRQAHGPSVQQAIEDAIFAVSGERAVIHAAGRTDAGVHGIAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AH D+ ++  P  L +ALNA L+    I+IL    V   +HARFS + RSY+YRI  R+
Sbjct: 61  RAHADIAKDMAPFRLMEALNARLR-PHPIAILACEAVPDDWHARFSCVGRSYVYRIANRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL  E G  W + + LD + M+ AAQ LVGRHDFTTFRS HCQA SP++T+D  DV   
Sbjct: 120 APLTWENGLVWRVIQPLDTDAMQEAAQLLVGRHDFTTFRSAHCQAESPVKTLDRLDVERS 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARSFLH Q+RS VG L LVG G+W+  DLE A  A+DR   G  APP+GLY
Sbjct: 180 GDRLAIYAEARSFLHHQVRSMVGCLALVGMGRWSIGDLEAARDARDRAALGLNAPPDGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FVRARY 245


>gi|254487927|ref|ZP_05101132.1| tRNA pseudouridine synthase A [Roseobacter sp. GAI101]
 gi|214044796|gb|EEB85434.1| tRNA pseudouridine synthase A [Roseobacter sp. GAI101]
          Length = 256

 Score =  244 bits (623), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 117/251 (46%), Positives = 166/251 (66%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEYNG+ Y GWQRQ   +++QG IE A+  V      +  AGRTD GVHAL Q
Sbjct: 1   MYRYALKIEYNGAPYVGWQRQIGLATVQGVIEDALAKVEPRAHKIAAAGRTDGGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ R+W P  L +ALN ++K  + +++++ + V  +FHARFSA  R Y +RI+ R+
Sbjct: 61  VAHCDMERDWDPFRLSEALNFHMK-PNPVAVVDCAPVGPEFHARFSAQERRYQFRILVRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G  W + K LD + MR  A+HL+G+HDFTTFRS  CQA++P++T+D  D+++ 
Sbjct: 120 APATHQAGLVWQVKKPLDLDAMRAGARHLIGQHDFTTFRSTICQAATPVKTVDRIDISAV 179

Query: 181 GNL----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             L    + + V ARSFLH Q+RSFVG+L+ VG G  T  D++    A+DR+ CGP++PP
Sbjct: 180 ETLGGLEVHLDVRARSFLHNQVRSFVGTLERVGAGSLTPDDVKVMRDARDRQACGPVSPP 239

Query: 237 EGLYFDSVEYS 247
            GLY   V+Y 
Sbjct: 240 HGLYLAHVDYP 250


>gi|192289057|ref|YP_001989662.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris TIE-1]
 gi|192282806|gb|ACE99186.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris TIE-1]
          Length = 245

 Score =  244 bits (623), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 127/246 (51%), Positives = 168/246 (68%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q    S+QG++E A     GE V VHGAGRTD+GVHAL Q
Sbjct: 1   MPRYKLTIEYDGAPFCGWQLQPALPSVQGALEVAALATCGEAVRVHGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + +    L  ALNA+L+  + +++L   IV   F ARFSA+RR Y YRI  R+
Sbjct: 61  VAHVDIPKPFRADKLRDALNAHLR-PNPVAVLAAEIVPDTFEARFSAVRRHYRYRIANRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           + LAL+ G+ W +PK LD + M  AAQ L+G+HDFTTFR   CQA+SP +T+D  DV   
Sbjct: 120 SNLALDLGKVWRVPKQLDTDAMHRAAQVLIGKHDFTTFRDTECQAASPEKTLDVLDVVRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ ++I   ARS+LH+Q+RS VGSL  VG+G+WT+ DL  AL A+ R  CGP+APPEGLY
Sbjct: 180 GDAVDIITNARSYLHSQVRSMVGSLVWVGEGRWTADDLAAALAARRRSACGPVAPPEGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LMQVDY 245


>gi|163795438|ref|ZP_02189405.1| Pseudouridylate synthase [alpha proteobacterium BAL199]
 gi|159179424|gb|EDP63955.1| Pseudouridylate synthase [alpha proteobacterium BAL199]
          Length = 248

 Score =  244 bits (623), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 119/247 (48%), Positives = 164/247 (66%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ + GWQRQ NG+++QG+IE A+F  +G+ V V GAGRTD+GVHA  Q
Sbjct: 1   MTRYRLTVEYDGAPFVGWQRQDNGATVQGAIEDAVFAFSGQRVEVAGAGRTDTGVHAEGQ 60

Query: 61  VAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VAH DL  + +  V +  A+NA+L+      +         FHARFSAI RSY Y I+ R
Sbjct: 61  VAHIDLATDRFDAVTVMNAINAHLRPLPVAVVSASVAS-PDFHARFSAIWRSYRYVIVNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APLAL+ GRAW +   LD   M   A+ L+G HDFT+FR++HCQ+ SP++T+D   V+ 
Sbjct: 120 RAPLALDLGRAWSVLAPLDVAAMSAGAERLIGHHDFTSFRAVHCQSKSPMKTLDVLQVSR 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I +   ARSFLH Q+R+ VG+L+LVG+GKW   D+  AL+A+DR   GP AP +GL
Sbjct: 180 HGERIVVEARARSFLHHQVRNMVGTLRLVGEGKWQPDDVTAALKARDRVAAGPTAPADGL 239

Query: 240 YFDSVEY 246
              +V Y
Sbjct: 240 TLTAVGY 246


>gi|118589718|ref|ZP_01547123.1| tRNA pseudouridine synthase A [Stappia aggregata IAM 12614]
 gi|118437804|gb|EAV44440.1| tRNA pseudouridine synthase A [Stappia aggregata IAM 12614]
          Length = 266

 Score =  244 bits (622), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 121/246 (49%), Positives = 156/246 (63%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G  + GWQRQ N  S+Q  IE+A    +GE V + GAGRTD+GVHA  Q
Sbjct: 1   MPRYKLTVEYDGRPFSGWQRQANAPSVQAVIERAAKAFSGEEVTIGGAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H DL ++W    +  ALN + +  D + IL+ + + + F ARFSAIRRSY YRI  R 
Sbjct: 61  VCHVDLSKDWDARTVMGALNFHCQ-PDPVVILDAAEMHEGFDARFSAIRRSYRYRIHNRL 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL  + G AW +   LD + M  AAQ  VG HDFTTFR   CQA SP +T++ F V   
Sbjct: 120 PPLTHQLGLAWHVKVHLDADAMHAAAQEFVGHHDFTTFRHTRCQAKSPEKTLEEFRVYRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +     +RSFLH Q+RS VGSL+LVG+GKW   D+ KAL A+DR  CGP+AP +GLY
Sbjct: 180 GEFVIAECASRSFLHNQVRSMVGSLRLVGEGKWGPGDITKALAARDRNACGPVAPADGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LTRVDY 245


>gi|254501121|ref|ZP_05113272.1| tRNA pseudouridine synthase A [Labrenzia alexandrii DFL-11]
 gi|222437192|gb|EEE43871.1| tRNA pseudouridine synthase A [Labrenzia alexandrii DFL-11]
          Length = 272

 Score =  244 bits (622), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 119/246 (48%), Positives = 158/246 (64%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G  + GWQRQ N  S+Q  IE+AI   +GE V + GAGRTD+GVHA  Q
Sbjct: 1   MPRYKLTVEYDGRPFSGWQRQANAPSVQAVIERAIKAFSGEEVTIGGAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H DL ++W    +  ALN + +  D + IL+   + + F ARFSAIRR+Y YRI  R 
Sbjct: 61  VCHADLSKQWPTKTVMGALNFHCQ-PDPVVILDCEEMHEGFDARFSAIRRAYRYRIHNRL 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL  + G AW +   LD + M  AAQ  VG HDFTTFR   CQA SP +T++HF V   
Sbjct: 120 QPLTHQLGLAWHVKHELDADAMHQAAQEFVGHHDFTTFRHSRCQAKSPEKTLEHFSVYRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +     +RSFLH Q+RS VG+L+LVG+ +W   D+  AL+A+DRK CGP+AP +GLY
Sbjct: 180 GDFVIAECSSRSFLHNQVRSMVGTLRLVGEDRWGPGDITNALKARDRKACGPVAPADGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LTRVDY 245


>gi|149203831|ref|ZP_01880800.1| tRNA pseudouridine synthase A [Roseovarius sp. TM1035]
 gi|149142948|gb|EDM30990.1| tRNA pseudouridine synthase A [Roseovarius sp. TM1035]
          Length = 258

 Score =  243 bits (621), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 119/250 (47%), Positives = 164/250 (65%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQ +  S+QG++E A+  +      +  AGRTD+GVHA+ Q
Sbjct: 1   MPRYALRIEYDGAPFAGWQRQVDHPSVQGAVEAALARIEPGSHTIAAAGRTDAGVHAIAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL REW    L +ALN +LK    ++I     V + +HARFSA  R YL+R+++R+
Sbjct: 61  VAHCDLTREWGTFRLSEALNYHLK-PLPVAITACVRVAEDWHARFSANERRYLFRVMSRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--- 177
           AP+ L++GR W +   LD + MR  AQHL+G HDFTTFRS  CQA+SPI+T+D  ++   
Sbjct: 120 APVTLDRGRVWHVRPKLDIDAMRAGAQHLIGMHDFTTFRSTICQAASPIKTLDAIEISEH 179

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
            ++ G  I  R+ ARSFLH Q+RS VG+L+ VG G W   ++  AL A+DR  CGP+ PP
Sbjct: 180 ESAMGPEIHFRLRARSFLHNQVRSIVGTLERVGAGSWHPDEVRAALNARDRAACGPVCPP 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLAGVSY 249


>gi|260431135|ref|ZP_05785106.1| tRNA pseudouridine synthase A [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260414963|gb|EEX08222.1| tRNA pseudouridine synthase A [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 255

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 123/251 (49%), Positives = 159/251 (63%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY G  + GWQRQK   S+QG+IE A+  +      +  AGRTD+GVHAL Q
Sbjct: 1   MPRYALKVEYQGEPFAGWQRQKELPSVQGAIEAALSKLQPGSHTIAAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W P  L +ALN +LK    ++IL  + V   +HARFSAI R YL+RI+ R+
Sbjct: 61  VAHCDLEKDWDPFRLSEALNYHLK-PLPVAILKAAQVADDWHARFSAIERQYLFRILIRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   +KG+ W I   LD   M+  A  L+GRHDFTTFRS  CQA+SP++T+D   V   
Sbjct: 120 APATHDKGQVWQIGHPLDVAAMQEGADMLIGRHDFTTFRSSICQAASPVKTLDELRVEQV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  +   V ARSFLH Q+RSFVG+L+ VG G WT  D+  AL+A DR  CGP+ PP
Sbjct: 180 QGFSGPEVHFHVRARSFLHNQVRSFVGTLERVGAGAWTPQDVRDALEATDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLARVGYP 250


>gi|39933700|ref|NP_945976.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris CGA009]
 gi|42559720|sp|P60352|TRUA_RHOPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|39647546|emb|CAE26067.1| putative tRNA-pseudouridine synthase [Rhodopseudomonas palustris
           CGA009]
          Length = 248

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 126/246 (51%), Positives = 168/246 (68%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q    S+QG++E A     GE V VHGAGRTD+GVHAL Q
Sbjct: 4   MPRYKLTIEYDGAPFCGWQLQPALPSVQGALEAAALATCGEAVRVHGAGRTDAGVHALGQ 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + +    L  ALNA+L+  + +++L   IV   F ARFSA+RR Y YRI  R+
Sbjct: 64  VAHVDIPKPFRADKLRDALNAHLR-PNPVAVLAAEIVPDTFEARFSAVRRHYRYRIANRR 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           + LAL+ G+ W +PK LD + M  AAQ L+G+H+FTTFR   CQA+SP +T+D  DV   
Sbjct: 123 SNLALDLGKVWRVPKPLDTDAMHRAAQVLIGKHNFTTFRDTECQAASPEKTLDVLDVIRD 182

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ ++I   ARS+LH+Q+RS VGSL  VG+G+WT+ DL  AL A+ R  CGP+APPEGLY
Sbjct: 183 GDAVDIITNARSYLHSQVRSMVGSLVWVGEGRWTADDLAAALAARRRSACGPVAPPEGLY 242

Query: 241 FDSVEY 246
              V+Y
Sbjct: 243 LMQVDY 248


>gi|85373239|ref|YP_457301.1| tRNA pseudouridine synthase A [Erythrobacter litoralis HTCC2594]
 gi|123005078|sp|Q2NCT7|TRUA_ERYLH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|84786322|gb|ABC62504.1| tRNA pseudouridine synthase A [Erythrobacter litoralis HTCC2594]
          Length = 247

 Score =  242 bits (618), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 117/246 (47%), Positives = 165/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +E++G+ + G QRQK+G S+Q ++E+A      + + +H AGRTD+GVHAL  
Sbjct: 1   MTRFALTLEFDGTPFMGLQRQKHGPSVQQAVEEAARATLNQDITLHSAGRTDTGVHALGM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            +HFD   +  P  L   LNA+L+    I++ N  I+ + +HARF+ I RSY+YRII R+
Sbjct: 61  RSHFDAETDLTPFRLMGGLNAHLR-PHPIAVTNCEIMPEDWHARFACIGRSYVYRIINRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL +++ RAW +P+ LD E M+ AAQ LVG HDFTTFRS  CQA  P++++D  +V   
Sbjct: 120 APLTIDRKRAWQVPQQLDHEAMQRAAQLLVGTHDFTTFRSTQCQAKDPVKSLDRLEVERD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I +   ARSFLH Q+RS VG LKLVG G W   ++E+AL A+DR+  G  APP GLY
Sbjct: 180 GDEIRVHAEARSFLHHQVRSMVGCLKLVGQGTWREEEVEEALLARDRQRLGLNAPPHGLY 239

Query: 241 FDSVEY 246
           F + EY
Sbjct: 240 FVAAEY 245


>gi|91974561|ref|YP_567220.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris BisB5]
 gi|123749504|sp|Q13F20|TRUA_RHOPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91681017|gb|ABE37319.1| tRNA pseudouridine synthase A [Rhodopseudomonas palustris BisB5]
          Length = 245

 Score =  242 bits (617), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 126/246 (51%), Positives = 169/246 (68%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q    S+QG++E A     GE V VHGAGRTD+GVHAL Q
Sbjct: 1   MPRYKLTIEYDGAPFCGWQLQPVLPSVQGALEAAALATCGEAVRVHGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + +    L  ALNA+++    +++L+  IV   F ARFSAIRR Y YRI+ R+
Sbjct: 61  VAHLDIAKPFRADRLRDALNAHVR-PYPVAVLSTEIVPDSFEARFSAIRRHYRYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           + LALE G+ W +PK LD + M  AAQ L+G+HDFTTFR   CQA+SP +T+D  DV   
Sbjct: 120 SNLALEIGKVWRVPKPLDTDAMHRAAQVLIGKHDFTTFRDTECQAASPEKTLDVLDVVRS 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ ++I   ARS+LH+Q+RS VGSL  VG+G+W++ DL  AL A+ R  CGP+APP+GLY
Sbjct: 180 GDCVDIITSARSYLHSQVRSMVGSLVWVGEGRWSADDLAAALAARRRSACGPVAPPDGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVKVDY 245


>gi|163742263|ref|ZP_02149651.1| tRNA pseudouridine synthase A [Phaeobacter gallaeciensis 2.10]
 gi|161384593|gb|EDQ08974.1| tRNA pseudouridine synthase A [Phaeobacter gallaeciensis 2.10]
          Length = 257

 Score =  242 bits (617), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 117/250 (46%), Positives = 166/250 (66%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+G+ + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRFALKVEYHGAPFAGWQRQKDQPSVQGAIENALARLEPGPHTIAAAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+V++W P  L +ALN +LK S  ++I++ + V+  +HARFSA+ R YL+RI+ R+
Sbjct: 61  VAHCDMVKDWDPFRLSEALNFHLKPS-PVAIVDCARVEDDWHARFSAVERQYLFRILIRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G+ W +   LD   M+ AA HL+G+HDFTTFRS  CQA+SP++T+D   +   
Sbjct: 120 APATHDAGQVWQLNHDLDAGAMQEAANHLIGQHDFTTFRSSICQAASPLKTLDELRIERV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I   V ARSFLH Q+RSFVG+L+ VG G W+  D++ AL+A+DR  CGP+ P 
Sbjct: 180 QGFSGPEIHFHVRARSFLHNQVRSFVGTLERVGAGAWSPEDVKSALEAEDRAACGPVCPG 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLARVGY 249


>gi|297182649|gb|ADI18807.1| pseudouridylate synthase [uncultured SAR11 cluster bacterium
           HF4000_37C10]
          Length = 245

 Score =  241 bits (616), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 115/246 (46%), Positives = 165/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ QKNG SIQ  ++ AIF  + E VVV GAGRTDSGVHAL Q
Sbjct: 1   MQRYKIKIEYDGTPFVGWQFQKNGPSIQEVLQNAIFNFSKEKVVVTGAGRTDSGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL ++         +N ++  +  +++L ++   K+FHARF A +R+Y Y II RQ
Sbjct: 61  VAHFDLKKKIKKKSFLPGVNQHIG-NKPVTVLKINKTSKKFHARFDAKKRTYQYTIINRQ 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +PLAL+K +AW I K LD + M+  A+ L+G HDF+TFR+  C A SPI+T+++  V   
Sbjct: 120 SPLALQKNKAWHIRKKLDVKAMKKGAKLLLGTHDFSTFRASSCGAKSPIKTMENISVKKN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I ++  +RSFL  Q+RS VGS+K +GDGKW   D +K+ ++++R +C P AP  GLY
Sbjct: 180 KDKITLKFTSRSFLQQQVRSMVGSIKYLGDGKWKLDDFKKSFKSKNRLKCAPPAPACGLY 239

Query: 241 FDSVEY 246
              ++Y
Sbjct: 240 LTKIKY 245


>gi|146276554|ref|YP_001166713.1| tRNA pseudouridine synthase A [Rhodobacter sphaeroides ATCC 17025]
 gi|166228756|sp|A4WPU4|TRUA_RHOS5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145554795|gb|ABP69408.1| tRNA pseudouridine synthase A [Rhodobacter sphaeroides ATCC 17025]
          Length = 257

 Score =  241 bits (615), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 122/251 (48%), Positives = 167/251 (66%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQ    S+QG+IE A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALKIEYDGAPFAGWQRQAVLPSVQGAIEAALGRLEPGPHTIAAAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W P  L  ALNA+LK    ++++  + V + FHARFSAI R YL+R++ R+
Sbjct: 61  VAHCDLGKDWDPFRLAGALNAHLK-PLPVAVVAAARVGEDFHARFSAIERRYLFRLLARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   ++GR W +P  LD   MR AA HLVGRHDFTTFR+I CQA+SP++T+D   + + 
Sbjct: 120 APEVHDRGRVWRVPHPLDGAAMREAAAHLVGRHDFTTFRAIGCQAASPVKTLDELTLETV 179

Query: 180 -FGNLIE--IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
              N +E   R+ ARSFLH Q+RS VG+L+ VG G W    +++AL+A+DR  CGP+ PP
Sbjct: 180 EVPNGVEYRFRLRARSFLHNQVRSIVGTLERVGAGAWAPDRVKEALEARDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLTGVGYP 250


>gi|254463862|ref|ZP_05077273.1| tRNA pseudouridine synthase A [Rhodobacterales bacterium Y4I]
 gi|206684770|gb|EDZ45252.1| tRNA pseudouridine synthase A [Rhodobacterales bacterium Y4I]
          Length = 255

 Score =  241 bits (615), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 118/250 (47%), Positives = 162/250 (64%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+G  + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVHAL Q
Sbjct: 1   MPRFALKVEYHGKPFAGWQRQKDLPSVQGAIEAALARLEPGEHTIAAAGRTDTGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ ++W P  L +ALN +LK  D ++I+  + VD  +HARFSA+ R YL+RI+ R+
Sbjct: 61  VAHCDMAKDWDPFRLSEALNYHLK-PDPVAIVGCARVDDDWHARFSAVERQYLFRILIRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G+ W +   LD + M+ AA +L+G HDFTTFRS  CQA SP++T+D   V   
Sbjct: 120 APATHDAGQVWQLSHELDADAMQEAANYLIGNHDFTTFRSSICQAQSPVKTLDELTVERV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I   V ARSFLH Q+RSFVG+L+ VG G W   D++ AL+A+DR  CGP+ P 
Sbjct: 180 QGFSGPEIHFHVRARSFLHNQVRSFVGTLERVGAGAWDPADVKAALEARDRAACGPVCPG 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLARVGY 249


>gi|149912589|ref|ZP_01901123.1| tRNA pseudouridine synthase A [Roseobacter sp. AzwK-3b]
 gi|149916040|ref|ZP_01904563.1| tRNA pseudouridine synthase A [Roseobacter sp. AzwK-3b]
 gi|149810114|gb|EDM69962.1| tRNA pseudouridine synthase A [Roseobacter sp. AzwK-3b]
 gi|149812995|gb|EDM72821.1| tRNA pseudouridine synthase A [Roseobacter sp. AzwK-3b]
          Length = 255

 Score =  241 bits (614), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 115/251 (45%), Positives = 161/251 (64%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ + GWQRQ    S+QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRYALKVEYDGAPFAGWQRQAEQPSVQGAIEAALARLEPGPHKIAAAGRTDAGVHGLAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DLV++W P  L  A+N +LK +    +    + +  +HARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDLVKDWEPFKLMGAVNYHLKPAPVAVVACAQVAE-DWHARFSALERRYLFRLLMRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  LE GR W +P+SLD   MR  A+HL+G+HDFTTFRS  CQA SP++T+D  ++   
Sbjct: 120 PPETLEAGRVWRVPQSLDVAAMREGARHLLGKHDFTTFRSSICQAKSPVKTLDALEIEEA 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  +   + ARSFLH Q+RS VG+L+ VG G W   D++ AL+A+DR  CGP+ PP
Sbjct: 180 EGLGGPELRFHLSARSFLHNQVRSIVGTLERVGAGSWAPEDVKTALEAKDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLAGVGYP 250


>gi|163738320|ref|ZP_02145735.1| Pseudouridylate synthase [Phaeobacter gallaeciensis BS107]
 gi|161388241|gb|EDQ12595.1| Pseudouridylate synthase [Phaeobacter gallaeciensis BS107]
          Length = 257

 Score =  240 bits (612), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 115/250 (46%), Positives = 166/250 (66%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+G+ + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRFALKVEYHGAPFAGWQRQKDQPSVQGAIEDALARLEPGPHTIAAAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+V++W P  L +ALN +LK +  ++I++ +  +  +HARFSA+ R YL+RI+ R+
Sbjct: 61  VAHCDMVKDWDPFRLSEALNFHLKPA-PVAIVDCARAEDDWHARFSAVERQYLFRILIRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G+ W +   LD  +M+ AA HL+G+HDFTTFRS  CQA+SP++T+D   +   
Sbjct: 120 APATHDAGQVWQLNHDLDAGSMQEAANHLIGQHDFTTFRSSICQAASPLKTLDELRIERV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I   V ARSFLH Q+RSFVG+L+ VG G W+  D++ AL+A+DR  CGP+ P 
Sbjct: 180 QGFSGPEIHFHVRARSFLHNQVRSFVGTLERVGAGAWSPEDVKSALEAEDRAACGPVCPG 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLARVGY 249


>gi|99082224|ref|YP_614378.1| tRNA pseudouridine synthase A [Ruegeria sp. TM1040]
 gi|122984147|sp|Q1GE00|TRUA_SILST RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|99038504|gb|ABF65116.1| Pseudouridylate synthase [Ruegeria sp. TM1040]
          Length = 259

 Score =  239 bits (611), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 116/250 (46%), Positives = 163/250 (65%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+G  + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRFALKVEYHGKPFAGWQRQKDQPSVQGAIEAALARIEPGEHTIAAAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL + W P  L +ALN +LK +  ++I++ ++VD ++HARFSA+ R YL+RI+ R+
Sbjct: 61  VAHCDLEKNWDPFRLSEALNYHLKPA-PVAIVDAALVDDEWHARFSAVERQYLFRILMRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   ++G+ W I   LD   M+  A  L+G HDFTTFRS  CQA+SP++T+D   V   
Sbjct: 120 APATHDEGQVWQIKHDLDVAAMQAGANMLLGNHDFTTFRSSICQAASPVKTLDELRVERV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  +   V ARSFLH Q+RSFVG+L+ VG G W+  D++ AL+A+DR  CGP+ P 
Sbjct: 180 QGLSGPEVHFHVRARSFLHNQVRSFVGTLERVGTGAWSPEDVKHALEAKDRAACGPVCPG 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLARVGY 249


>gi|254475915|ref|ZP_05089301.1| tRNA pseudouridine synthase A [Ruegeria sp. R11]
 gi|214030158|gb|EEB70993.1| tRNA pseudouridine synthase A [Ruegeria sp. R11]
          Length = 256

 Score =  239 bits (611), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 119/250 (47%), Positives = 162/250 (64%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+G+ + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRFALKVEYHGAPFAGWQRQKDQPSVQGAIEDALARLEPGPHTIAAAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + W P  L +ALN +LK +  ++I++ + VD  +HARFSAI R YL+RI+ R+
Sbjct: 61  VAHCDMAKAWDPFRLSEALNYHLKPA-PVAIVDCAQVDDDWHARFSAIERQYLFRILIRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G+ W +   LD   M+ AA HLVG+HDFTTFRS  CQA+SP++T+D   V   
Sbjct: 120 APATHDAGQVWQLSHDLDVAAMQEAADHLVGQHDFTTFRSSICQAASPLKTLDELRVERV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I   V ARSFLH Q+RSFVG+L+ VG G W   D++ AL+A DR  CGP+ P 
Sbjct: 180 QGFSGPEIHFHVRARSFLHNQVRSFVGTLERVGAGAWDPVDVKDALEACDRAACGPVCPG 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLARVGY 249


>gi|254441675|ref|ZP_05055168.1| tRNA pseudouridine synthase A [Octadecabacter antarcticus 307]
 gi|198251753|gb|EDY76068.1| tRNA pseudouridine synthase A [Octadecabacter antarcticus 307]
          Length = 256

 Score =  239 bits (611), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 120/251 (47%), Positives = 158/251 (62%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQ +  S+QG+IE A+  +      +  AGRTD+GVHAL Q
Sbjct: 1   MPRYALKIEYDGAPFCGWQRQTSDPSVQGAIEAALAKLEPRGHTIGAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + W    L +ALN +LK +  +SI+    V   +HARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDMDKTWDAFRLSEALNFHLKPA-PVSIVACVQVADDWHARFSALERRYLFRLVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL LE G+ W + + LD   M+  A  L+G HDFTTFRS  CQA SP+RT+D  D+   
Sbjct: 120 APLVLEAGKVWQVSQKLDGAAMQAGADRLLGHHDFTTFRSTVCQADSPMRTLDGLDIEQV 179

Query: 181 -----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                       V ARSFLH Q+RSFVG+L+ VG G WT  D+  AL A+DR  CGP+ P
Sbjct: 180 ARSDGAQEFRFHVRARSFLHNQVRSFVGTLERVGAGAWTRDDVSAALNARDRTACGPVCP 239

Query: 236 PEGLYFDSVEY 246
           P GLY  SV Y
Sbjct: 240 PHGLYLASVGY 250


>gi|86139183|ref|ZP_01057753.1| tRNA pseudouridine synthase A [Roseobacter sp. MED193]
 gi|85824027|gb|EAQ44232.1| tRNA pseudouridine synthase A [Roseobacter sp. MED193]
          Length = 258

 Score =  239 bits (611), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 118/251 (47%), Positives = 161/251 (64%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+G  + GWQRQK+  S+QG+IE+A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRFALKVEYHGKPFAGWQRQKDQPSVQGAIEEALAKLEPGPHTIAAAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL + W P  L +ALN +LK +  ++I++ ++VD ++HARFSAI R YL+RI+ R+
Sbjct: 61  VAHCDLQKPWSPFRLSEALNFHLKPA-PVAIVDCAVVDPEWHARFSAIERQYLFRILIRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G+ W I   LD E M+  A HL+G HDFTTFRS  CQA SP +T+D   +   
Sbjct: 120 APATHDAGQVWQINNDLDVERMQQGANHLLGNHDFTTFRSSICQAQSPQKTLDELRIERV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  +   V ARSFLH Q+RSFVG+L+ VG   WT  D++ AL+A DR  CGP+ P 
Sbjct: 180 QGLSGPEVHFHVRARSFLHNQVRSFVGTLERVGADAWTPQDVKSALEACDRAACGPVCPG 239

Query: 237 EGLYFDSVEYS 247
            GLY   V Y 
Sbjct: 240 HGLYLARVGYP 250


>gi|259417872|ref|ZP_05741791.1| tRNA pseudouridine synthase A [Silicibacter sp. TrichCH4B]
 gi|259346778|gb|EEW58592.1| tRNA pseudouridine synthase A [Silicibacter sp. TrichCH4B]
          Length = 278

 Score =  239 bits (611), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 121/250 (48%), Positives = 159/250 (63%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + +EY+G  + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 20  MPRIALKVEYHGKPFAGWQRQKDQPSVQGAIEAALAKLEPGEHTIAAAGRTDTGVHGLGQ 79

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W P  L +ALN +LK  D I+I++ + VD  +HARFSAI R YL+RI+ R+
Sbjct: 80  VAHCDLQKDWDPFRLSEALNYHLK-PDPIAIVDAARVDDDWHARFSAIERQYLFRILMRR 138

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G+ W I   LD E M+  A  L+G HDFTTFRS  CQA+SP++T+D   V   
Sbjct: 139 APATHDAGQVWQINHRLDVEAMQAGADMLLGNHDFTTFRSSICQAASPVKTLDELRVEQV 198

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  +   V ARSFLH Q+RSFVG+L+ VG G WT  D+  AL A+DR  CGP+ P 
Sbjct: 199 QGLSGPEVHFHVRARSFLHNQVRSFVGTLERVGAGAWTPEDVRDALAAKDRAACGPVCPG 258

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 259 HGLYLARVGY 268


>gi|329849464|ref|ZP_08264310.1| tRNA pseudouridine synthase A [Asticcacaulis biprosthecum C19]
 gi|328841375|gb|EGF90945.1| tRNA pseudouridine synthase A [Asticcacaulis biprosthecum C19]
          Length = 257

 Score =  239 bits (610), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 120/246 (48%), Positives = 159/246 (64%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  +IEY+G  Y G+Q Q +  ++Q S+E+AI   +GE + +  AGRTD+GVHA  Q
Sbjct: 1   MPRYRCLIEYDGRPYKGFQAQGDHPTVQASLERAILGFSGEALRITAAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V  FDL + +    +  A+NA+L   + +S+L    VD +F ARFSA  R YLYRI+TR+
Sbjct: 61  VVSFDLSKAFKADTVRDAMNAFLA-REPVSVLAAEQVDDEFSARFSATGRMYLYRILTRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP AL+ GR W + K LD E M  AA+ LVG HDFTTFR + CQA SP++T+D   V  F
Sbjct: 120 APPALDMGRVWHVKKPLDAEVMAQAAKALVGTHDFTTFRHVECQAKSPVKTLDIARVKRF 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I +   ARSFLH Q+RS  G+L   G G+W   D+ +AL A+DR  CG +APPEGLY
Sbjct: 180 GDEIHLVFAARSFLHRQVRSMTGTLVEAGIGRWDIADVAEALAAKDRAACGQVAPPEGLY 239

Query: 241 FDSVEY 246
              V Y
Sbjct: 240 LTHVTY 245


>gi|114769437|ref|ZP_01447063.1| tRNA pseudouridine synthase A [alpha proteobacterium HTCC2255]
 gi|114550354|gb|EAU53235.1| tRNA pseudouridine synthase A [alpha proteobacterium HTCC2255]
          Length = 255

 Score =  239 bits (610), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 117/250 (46%), Positives = 161/250 (64%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G  Y GWQRQ++  S+Q +IE AI  +  E   + GAGRTD+GVHA  Q
Sbjct: 1   MPRYALKVEYDGKPYHGWQRQRDVPSVQQTIEIAISKIAPEKPEIQGAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +AHFDL + W    L +A+N +L+  + ISI   SIV   FHARFSA  R Y++R+++R+
Sbjct: 61  IAHFDLNKPWDSFRLSEAINYHLR-PEPISITKCSIVADDFHARFSAKERRYVFRLLSRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP  ++ G  W I   LD E M+  A++LVG+HDFTTFRS  CQA SPI+++    +   
Sbjct: 120 APAIVDVGWVWQIQHDLDLELMQEGAKYLVGKHDFTTFRSSICQAQSPIKSLKEISIKEI 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G   E  ++ARSFLH Q+RSF+G+L+ VG G W    + +AL A+DR +CGP+ PP
Sbjct: 180 SLEHGKEFEFTIIARSFLHNQVRSFIGTLERVGSGSWDPERVHEALIAKDRSKCGPVCPP 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLAQVSY 249


>gi|148258520|ref|YP_001243105.1| tRNA pseudouridine synthase A [Bradyrhizobium sp. BTAi1]
 gi|166228680|sp|A5ESQ5|TRUA_BRASB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|146410693|gb|ABQ39199.1| tRNA pseudouridine synthase A [Bradyrhizobium sp. BTAi1]
          Length = 245

 Score =  239 bits (610), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 123/246 (50%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q+   S+QG++E A+    G    VHG+GRTD+GVHA  Q
Sbjct: 1   MPRYKLTIEYDGTPFCGWQLQETLPSVQGALEAAVQATCGVPTRVHGSGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ +++ P  L  ALNA+L+  + +++L   IV   F ARFSA +R Y YRI+ R+
Sbjct: 61  VAHCDIAKDFRPDKLRDALNAHLR-PNPVAVLEAEIVSDTFEARFSARKRHYRYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           + LALE GR W +P+ LD + M  AAQ L+GRHDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 SNLALEVGRVWRVPQRLDSDAMHAAAQRLIGRHDFTTFRDTECQAKSPEKTLDQLDVVRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARS+LH+Q+RS VGSL  VG G+W++ DL  AL A++R  CG +APPEGLY
Sbjct: 180 GDAVTILTSARSYLHSQVRSMVGSLVWVGQGRWSADDLAAALAARNRAACGVVAPPEGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVKVDY 245


>gi|56697975|ref|YP_168346.1| tRNA pseudouridine synthase A [Ruegeria pomeroyi DSS-3]
 gi|62901184|sp|Q5LNR0|TRUA_SILPO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56679712|gb|AAV96378.1| tRNA pseudouridine synthase A [Ruegeria pomeroyi DSS-3]
          Length = 262

 Score =  239 bits (609), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 119/250 (47%), Positives = 159/250 (63%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY G+ + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRYALKVEYLGTPFAGWQRQKDLPSVQGAIETALARLEPGPHTIAAAGRTDAGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R+W P  L +ALN +LK    ++I   + V + +HARFSA  R YL+R++ R+
Sbjct: 61  VAHCDLTRDWDPFRLSEALNYHLK-PQPVAITAAARVAEDWHARFSATERQYLFRLLMRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G  W +   LD   M+ AA  L+GRHDFTTFRS  CQA+SP++T+D   V + 
Sbjct: 120 APATHDAGLVWQVGHRLDARAMQAAADLLLGRHDFTTFRSSICQAASPVKTLDELRVEAV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I   V ARSFLH Q+RSFVG+L+ VG G W   D+  AL+A+DR  CGP+ PP
Sbjct: 180 ESFSGPEIRFHVRARSFLHNQVRSFVGTLERVGAGAWAPEDVRSALEARDRAACGPVCPP 239

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 240 QGLYLARVGY 249


>gi|148556941|ref|YP_001264523.1| tRNA pseudouridine synthase A [Sphingomonas wittichii RW1]
 gi|166229840|sp|A5VDL9|TRUA_SPHWW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148502131|gb|ABQ70385.1| tRNA pseudouridine synthase A [Sphingomonas wittichii RW1]
          Length = 254

 Score =  238 bits (608), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 126/246 (51%), Positives = 160/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +E++G  + GWQRQ +G S+Q +IE+AI  VTGE  V+H AGRTD+ VH    
Sbjct: 1   MTRFRLTVEFDGRPFMGWQRQAHGPSVQQAIEEAITAVTGERAVIHAAGRTDARVHGRAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AH D+ +   P  L +ALNA L+ +  ++IL    V   +HARFS + R Y+YRI+ R+
Sbjct: 61  TAHADIAKPITPFRLKEALNARLRPA-PVAILACEPVAGDWHARFSCVGRRYVYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL  + G AW +   LD + M  AAQ LVGRHDFTTFRS HCQA SP++T+D  DV   
Sbjct: 120 APLTFDAGLAWQVAADLDDQAMHAAAQCLVGRHDFTTFRSAHCQAESPVKTLDRLDVRRS 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G LIEI   ARSFLH Q+RS VG L LVG G+WT+ DL  AL A DR   G  APP+GLY
Sbjct: 180 GELIEIEAAARSFLHHQVRSMVGCLALVGRGRWTAADLADALAAADRARLGLNAPPDGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FMEAVY 245


>gi|159044486|ref|YP_001533280.1| tRNA pseudouridine synthase A [Dinoroseobacter shibae DFL 12]
 gi|189030132|sp|A8LNZ7|TRUA_DINSH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157912246|gb|ABV93679.1| pseudouridine synthase A [Dinoroseobacter shibae DFL 12]
          Length = 257

 Score =  238 bits (608), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 114/250 (45%), Positives = 162/250 (64%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IEY+G+ + GWQRQ+   S+QG++E A+  +  +   +  AGRTD+GVHAL Q
Sbjct: 1   MPRFALKIEYDGAPFAGWQRQREQPSVQGAVEAALRGLQPDHAGIAAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R+W P  L +ALNA+L+ +    +     V + FHARFSA+ RSYL+R++ R+
Sbjct: 61  VAHVDLARDWDPFRLSEALNAHLRPAPVAVLAAAR-VGEDFHARFSALERSYLFRLLVRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS- 179
           AP   + G  W +   LD E MR  A++L+G+HDFTTFRS  CQA+SP++T+D   +   
Sbjct: 120 APATHDAGLVWRVMNPLDVEAMREGAKYLIGKHDFTTFRSTMCQAASPVKTLDEITIEES 179

Query: 180 ---FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      + ARSFLH Q+RS VG+L+ VG G W   D++ AL+A+DR  CGP+  P
Sbjct: 180 PRDAGTEFRFHLRARSFLHNQVRSIVGTLERVGAGAWDPADVKTALEARDRAACGPVCAP 239

Query: 237 EGLYFDSVEY 246
           +GLY  +V Y
Sbjct: 240 QGLYLRAVRY 249


>gi|126737019|ref|ZP_01752754.1| tRNA pseudouridine synthase A [Roseobacter sp. SK209-2-6]
 gi|126721604|gb|EBA18307.1| tRNA pseudouridine synthase A [Roseobacter sp. SK209-2-6]
          Length = 255

 Score =  238 bits (607), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 119/250 (47%), Positives = 162/250 (64%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+G  + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRFALKVEYHGKPFAGWQRQKDLPSVQGAIEDALSRLEPGAHTIAAAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W P  L +ALN +LK +  ++IL+ + VD+ +HARFSAI R YL+RI+ R+
Sbjct: 61  VAHCDLQKDWDPFRLSEALNYHLKPA-PVAILDCAGVDEDWHARFSAIERQYLFRILMRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G+ W I   LD   M+ AA HL+G HDFTTFRS  CQA+SP +T+D   + + 
Sbjct: 120 APATHDAGQVWQINHELDVAAMQEAADHLIGNHDFTTFRSSICQAASPQKTLDELRIETV 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  +   V ARSFLH Q+RSFVG+L+ VG G W   D++ AL+A DR  CGP+ P 
Sbjct: 180 QGLSGPEVHFHVRARSFLHNQVRSFVGTLERVGAGSWEPLDVKHALEACDRSACGPVCPG 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLARVGY 249


>gi|85703371|ref|ZP_01034475.1| tRNA pseudouridine synthase A [Roseovarius sp. 217]
 gi|85672299|gb|EAQ27156.1| tRNA pseudouridine synthase A [Roseovarius sp. 217]
          Length = 257

 Score =  238 bits (607), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 119/250 (47%), Positives = 162/250 (64%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQ +  S+QG+IE A+  +      +  AGRTD+GVHAL Q
Sbjct: 1   MPRYALKIEYDGAPFAGWQRQVDHPSVQGAIEAALGRIEPGPHTIAAAGRTDAGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R+W    L +ALN +LK    ++I   + V + +HARFSA  R YL+RI++R+
Sbjct: 61  VAHCDLPRDWGTFRLSEALNYHLK-PLPVAITGCARVPEDWHARFSATERQYLFRILSRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP+ L++GR W +   LD + MR  A HL+G HDFTTFRS  CQA+SPI+T+D  +++  
Sbjct: 120 APVTLDQGRVWHVRPMLDIDAMRAGAAHLIGTHDFTTFRSTICQAASPIKTLDSIEISEH 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  I  ++ ARSFLH Q+RS VG+L+ VG G W    +  AL A+DR  CGP+ PP
Sbjct: 180 STPTGTEIHFQLRARSFLHNQVRSIVGTLERVGAGSWHPDQVRGALDARDRAACGPVCPP 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 YGLYLAHVVY 249


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

 Score =  238 bits (606), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 113/246 (45%), Positives = 162/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ QKNG SIQ  ++ AIF  + E VVV GAGRTDSGVHAL Q
Sbjct: 1   MQRYKIKIEYDGTPFVGWQFQKNGQSIQEVLQNAIFNFSKEKVVVTGAGRTDSGVHALAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL ++         +N ++  +  +++L ++   K+FHARF A +R+Y Y II RQ
Sbjct: 61  VAHFDLKKKIKKKSFLPGINQHIG-NKPVTVLKINKTSKKFHARFDAKKRTYQYTIINRQ 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +PL L+K +AW I K LD   M+  A+ L+G HDF+TFR+  C A SPI+T+++  +   
Sbjct: 120 SPLTLQKNKAWHIRKKLDVRAMKKGAKLLLGTHDFSTFRASSCGAKSPIKTMENISIKKN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I ++ ++RSFL  Q+RS VG +K +GDGKW   D +K+ +++ R EC P AP  GLY
Sbjct: 180 KDKITLKFISRSFLQQQVRSMVGCIKYLGDGKWKLEDFKKSFKSKCRLECAPPAPASGLY 239

Query: 241 FDSVEY 246
              ++Y
Sbjct: 240 LAKIKY 245


>gi|146337887|ref|YP_001202935.1| tRNA pseudouridine synthase A [Bradyrhizobium sp. ORS278]
 gi|166228681|sp|A4YLC1|TRUA_BRASO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|146190693|emb|CAL74697.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Bradyrhizobium sp. ORS278]
          Length = 245

 Score =  238 bits (606), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 123/246 (50%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q+   S+QG +E A+    G    VHG+GRTD+GVHA  Q
Sbjct: 1   MPRYKLTIEYDGAPFCGWQLQETLPSVQGVLEAAVQATCGVPTRVHGSGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ +E+ P  L  ALNA+L+  + +++L+  IV   F ARFSA +R Y YRI+ R+
Sbjct: 61  VAHCDIDKEFRPDKLRDALNAHLR-PNPVAVLDAQIVPDTFEARFSARKRHYRYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           + LALE GR W +P+ LD + M +AAQ L+G+HDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 SNLALEVGRVWRVPQRLDSDAMHVAAQRLIGKHDFTTFRDTECQAKSPEKTLDQLDVVRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I   ARS+LH+Q+RS VGSL  VG G+W++ DL  AL A+ R  CG +APPEGLY
Sbjct: 180 GDAVTIITSARSYLHSQVRSMVGSLVWVGQGRWSADDLAAALAARRRAACGVVAPPEGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVQVDY 245


>gi|27383218|ref|NP_774747.1| tRNA pseudouridine synthase A [Bradyrhizobium japonicum USDA 110]
 gi|27356392|dbj|BAC53372.1| tRNA pseudouridine synthase I [Bradyrhizobium japonicum USDA 110]
          Length = 252

 Score =  237 bits (605), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 124/246 (50%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ +FGWQ Q    S+QG++E A+  +TG  + VHGAGRTD+GVHA  Q
Sbjct: 8   MPRYKLTIEYDGAPFFGWQVQDTLPSVQGALEAAVKAMTGADLRVHGAGRTDAGVHARGQ 67

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ +++ P      LNA+L+    I++L   IV   F ARFSA++R Y YRI+  +
Sbjct: 68  VAHVDIEKQFPPGRFRDGLNAHLR-PHPIAVLEAEIVPDTFEARFSAVKRHYRYRIVNTR 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A LAL+ G AW +P+ LD + M  AA+ L+G+HDFTTFR   CQA SP +T+D  DV   
Sbjct: 127 ANLALDIGHAWRVPRRLDSDAMHAAARRLLGKHDFTTFRDTECQAKSPEKTLDQLDVLRD 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I   ARSFLH+Q+RS VGSL  VG+G+WT+ DL  AL A++R  CG +APP+GLY
Sbjct: 187 GREITIITSARSFLHSQVRSMVGSLVWVGEGRWTADDLSAALAARNRAACGIVAPPDGLY 246

Query: 241 FDSVEY 246
              V+Y
Sbjct: 247 LVKVDY 252


>gi|254418055|ref|ZP_05031779.1| tRNA pseudouridine synthase A [Brevundimonas sp. BAL3]
 gi|196184232|gb|EDX79208.1| tRNA pseudouridine synthase A [Brevundimonas sp. BAL3]
          Length = 247

 Score =  237 bits (605), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 116/246 (47%), Positives = 157/246 (63%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ Y G+Q Q +  ++QG++E AI   +GE + +  AGRTD+GVHA  Q
Sbjct: 1   MPRYKLTLEYDGTAYNGFQAQADQPTVQGAVEAAILAFSGERIRIAAAGRTDTGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H DL R+W    +  A+NA+L   D   +      D  +HARFSA  R YLYRI+ R+
Sbjct: 61  VIHADLERDWPVDTVLNAVNAHLIKQDVCVLSAEYAPDPDWHARFSATGRGYLYRILNRR 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               LE+ R W + KSLD E M  AAQ LVG HDFTTFR + CQ+ SP++T+D   V+ F
Sbjct: 121 PQPVLERDRVWHVKKSLDAEAMHQAAQVLVGLHDFTTFRDVGCQSKSPVKTLDVARVSRF 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + +   ARSFLH Q+RS  G+L  VG G+WT+ D++ AL+A+DR  CGP+AP  GLY
Sbjct: 181 GEEVHLVFQARSFLHRQVRSMAGTLVEVGLGRWTAHDVKAALEAKDRARCGPVAPSAGLY 240

Query: 241 FDSVEY 246
              V Y
Sbjct: 241 LSGVRY 246


>gi|254454857|ref|ZP_05068294.1| tRNA pseudouridine synthase A [Octadecabacter antarcticus 238]
 gi|198269263|gb|EDY93533.1| tRNA pseudouridine synthase A [Octadecabacter antarcticus 238]
          Length = 256

 Score =  237 bits (605), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 120/251 (47%), Positives = 159/251 (63%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQ +  S+QG+IE A+  +      +  AGRTD+GVHAL Q
Sbjct: 1   MPRYALKIEYDGAPFCGWQRQTSDPSVQGAIEAALAKLEPREHKIGAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + W    L +ALN +LK +  ISI+  + V   +HARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDMDKAWDAFRLSEALNFHLKPA-PISIVACAQVSDDWHARFSALERRYLFRLVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL LE G+ W + + LD   M+  A  L+G HDFTTFRS  CQA SP+RT+D   V   
Sbjct: 120 APLVLEVGKVWQVGQKLDGALMQAGADRLLGHHDFTTFRSTVCQADSPMRTLDGLKVQQV 179

Query: 181 GNL-----IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
             +      +  V ARSFLH Q+RSFVG+L+ VG G WT  D+  AL A+DR  CGP+ P
Sbjct: 180 TRVDGAQEFQFHVRARSFLHNQVRSFVGTLERVGAGAWTPDDVTAALNARDRTACGPVCP 239

Query: 236 PEGLYFDSVEY 246
           P GLY   V Y
Sbjct: 240 PHGLYLAGVSY 250


>gi|114763999|ref|ZP_01443240.1| tRNA pseudouridine synthase A [Pelagibaca bermudensis HTCC2601]
 gi|114543591|gb|EAU46605.1| tRNA pseudouridine synthase A [Roseovarius sp. HTCC2601]
          Length = 255

 Score =  237 bits (605), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 114/251 (45%), Positives = 158/251 (62%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G  + GWQRQ +  S+QG+IE A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALLVEYDGRPFAGWQRQADQPSVQGAIEAALARLEKRDHTIAAAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + W P  L +ALN +LK +  ++I   + V   +HARFSA  R YL+R++ R+
Sbjct: 61  VAHCDMEKAWDPFRLSEALNFHLKPA-PVAIRACAAVSDDWHARFSAHERRYLFRLLVRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--- 177
           AP  LE G+ W +   L  E MR  A HL+G+HDFTTFRS  CQA+SP++T+D   +   
Sbjct: 120 APATLEAGQVWRVMNPLSLEAMRAGAAHLIGQHDFTTFRSTMCQAASPVKTMDEIRIEQT 179

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      + ARSFLH Q+RS VG+L+ VG G W   D+  AL+A+DR  CGP+ PP
Sbjct: 180 DTGAGTEFRFHLRARSFLHNQVRSIVGTLERVGAGSWAPEDVRSALEARDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y+
Sbjct: 240 DGLYLMGVGYA 250


>gi|42559808|sp|Q89BP1|TRUA_BRAJA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
          Length = 245

 Score =  237 bits (604), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 124/246 (50%), Positives = 166/246 (67%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ +FGWQ Q    S+QG++E A+  +TG  + VHGAGRTD+GVHA  Q
Sbjct: 1   MPRYKLTIEYDGAPFFGWQVQDTLPSVQGALEAAVKAMTGADLRVHGAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ +++ P      LNA+L+    I++L   IV   F ARFSA++R Y YRI+  +
Sbjct: 61  VAHVDIEKQFPPGRFRDGLNAHLR-PHPIAVLEAEIVPDTFEARFSAVKRHYRYRIVNTR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A LAL+ G AW +P+ LD + M  AA+ L+G+HDFTTFR   CQA SP +T+D  DV   
Sbjct: 120 ANLALDIGHAWRVPRRLDSDAMHAAARRLLGKHDFTTFRDTECQAKSPEKTLDQLDVLRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I   ARSFLH+Q+RS VGSL  VG+G+WT+ DL  AL A++R  CG +APP+GLY
Sbjct: 180 GREITIITSARSFLHSQVRSMVGSLVWVGEGRWTADDLSAALAARNRAACGIVAPPDGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LVKVDY 245


>gi|89070283|ref|ZP_01157602.1| tRNA pseudouridine synthase A [Oceanicola granulosus HTCC2516]
 gi|89044122|gb|EAR50283.1| tRNA pseudouridine synthase A [Oceanicola granulosus HTCC2516]
          Length = 257

 Score =  237 bits (604), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 118/252 (46%), Positives = 161/252 (63%), Gaps = 6/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G  Y GWQRQ   +++QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRYALKVEYDGGPYAGWQRQDGPATVQGAIEAALARLEPGPHTIAAAGRTDAGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA  DL + W P  L +ALN +LK +  I+I+  + V   +HARFSA  R YL+R++ R+
Sbjct: 61  VAQADLAKAWEPFRLAEALNYHLKPA-PIAIVACARVADDWHARFSANERRYLFRLVARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL  E+G+ W + + LD   M+  A  LVG HDFTTFRS  CQA SP++T+D   V + 
Sbjct: 120 APLPFERGQVWKVNQPLDAAAMQAGADLLVGHHDFTTFRSSICQADSPVKTLDELTVETV 179

Query: 181 ---GNLIEIR--VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                  E R  V ARSFLH Q+RSFVG+L+ VG G W    + +AL A++RK CGP+AP
Sbjct: 180 TRPDGYPEYRFHVRARSFLHNQVRSFVGTLERVGAGAWPPERVGEALAARERKACGPVAP 239

Query: 236 PEGLYFDSVEYS 247
           P+GLY  +V+Y 
Sbjct: 240 PQGLYLAAVKYP 251


>gi|254293237|ref|YP_003059260.1| tRNA pseudouridine synthase A [Hirschia baltica ATCC 49814]
 gi|254041768|gb|ACT58563.1| tRNA pseudouridine synthase A [Hirschia baltica ATCC 49814]
          Length = 247

 Score =  234 bits (598), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 119/246 (48%), Positives = 158/246 (64%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + IEY+GS Y GWQRQK   S+Q  +E+AI    GE V VHGAGRTD+GVHA+ Q
Sbjct: 1   MARFKLTIEYDGSPYVGWQRQKTHRSVQQVLEEAIPKFAGETVTVHGAGRTDAGVHAMGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL +E+    +  A+N ++K  + +SIL    V  +FHARFSA  R Y+YRII R+
Sbjct: 61  VAHIDLSKEFTTDKVRDAMNHFMK-DEPVSILLAEEVSDEFHARFSAYARHYIYRIIDRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A L  ++  AW     +D + M  AAQ LVG+HDF+TFR   CQA SP++T+   +V   
Sbjct: 120 ADLTFDRNLAWRAMSPVDADAMHEAAQCLVGKHDFSTFRDAQCQAESPVKTLSKIEVIRD 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I V A SFLH Q+RS  GSL  +G GK   + +++ L A DR  CG +APP+GLY
Sbjct: 180 GDEINIYVSAPSFLHRQVRSITGSLMEIGRGKKPISWMQEILGAADRSRCGTVAPPDGLY 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LSQVDY 245


>gi|260426957|ref|ZP_05780936.1| tRNA pseudouridine synthase A [Citreicella sp. SE45]
 gi|260421449|gb|EEX14700.1| tRNA pseudouridine synthase A [Citreicella sp. SE45]
          Length = 255

 Score =  233 bits (595), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 112/251 (44%), Positives = 157/251 (62%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G  + GWQRQ +  S+QG+IE A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALLVEYDGGPFAGWQRQADQPSVQGAIEAALARLEPREHTIAAAGRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + W P  L +ALN +LK +  ++I   + V   +HARFSA+ R Y +R++ R+
Sbjct: 61  VAHCDMAKPWDPFRLSEALNFHLKPA-PVAIRACAAVADDWHARFSAVERRYTFRLLARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP  LE G+ W +   LD   M+  A HL+G HDFTTFRS  CQA+SP++T+D   +   
Sbjct: 120 APATLEAGQVWRVMNPLDLGAMQEGAAHLLGLHDFTTFRSTMCQAASPVKTLDEIRIEEC 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      + ARSFLH Q+RS VG+L+ VG G W   D++ AL+A+DR  CGP+ PP
Sbjct: 180 DTGAGPEYRFHLRARSFLHNQVRSIVGTLERVGAGSWAPEDVKHALEARDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 DGLYLTGVGYP 250


>gi|170742366|ref|YP_001771021.1| tRNA pseudouridine synthase A [Methylobacterium sp. 4-46]
 gi|238688005|sp|B0UP40|TRUA_METS4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|168196640|gb|ACA18587.1| tRNA pseudouridine synthase A [Methylobacterium sp. 4-46]
          Length = 250

 Score =  233 bits (593), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 113/246 (45%), Positives = 156/246 (63%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+GSG+ GWQRQ    ++Q ++E+AI    G  V VH AGRTD+GVHA  Q
Sbjct: 1   MPRYKLVVEYDGSGFAGWQRQAADRTVQQALEEAIARFAGAPVRVHCAGRTDAGVHATHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H DL R+W    +  A NA+L+  + +++++   V   F AR SA+RR Y YRI+ R+
Sbjct: 61  VVHLDLDRDWRTDTVRDASNAHLR-PEPVAVVSAERVRPDFDARHSALRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P AL +   W +P SLD   M  AAQ L+GRHDF+ FR+  CQA+SP+RT+D  DV   
Sbjct: 120 SPPALGRAYLWHVPWSLDAHAMHAAAQTLLGRHDFSAFRAAECQANSPVRTLDQLDVARI 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I +   ARSFLH Q+R  VG+L L G G+  +  +   L ++DR  CGPLAP  GL 
Sbjct: 180 GDEILVATSARSFLHHQVRGMVGTLMLAGCGRLDAAGVRAVLDSRDRTRCGPLAPAAGLT 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LTGVDY 245


>gi|84503354|ref|ZP_01001423.1| tRNA pseudouridine synthase A [Oceanicola batsensis HTCC2597]
 gi|84388264|gb|EAQ01215.1| tRNA pseudouridine synthase A [Oceanicola batsensis HTCC2597]
          Length = 255

 Score =  232 bits (592), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 111/251 (44%), Positives = 161/251 (64%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G+ + GWQRQ +  S+QG+IE A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRYALQVEYHGAPFAGWQRQADQPSVQGAIEAALARLEPGPHTIAAAGRTDAGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA  DL ++W P  L +ALN +L+ +  ++I   + V + +HARFSA+ R Y++R++ R+
Sbjct: 61  VAQCDLEKDWDPFRLSEALNHHLRPA-PVAIRACARVAEDWHARFSALERRYMFRLLMRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP   + G  W +P  LD E +R  A HLVG HDFTTFRS+ CQA SP++T+D   +   
Sbjct: 120 APATHDAGLVWQVPHRLDPEAIRAGAAHLVGHHDFTTFRSVICQAKSPVKTLDEIRIEEH 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G  +   + ARSFLH Q+RS VG+L+ VG G+W  + + +AL+A+DR  CGP+ PP
Sbjct: 180 DGFSGPELRFHLRARSFLHNQVRSIVGTLERVGAGRWPPSRVAEALEARDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLVGVGYP 250


>gi|294085062|ref|YP_003551822.1| Pseudouridylate synthase [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292664637|gb|ADE39738.1| Pseudouridylate synthase [Candidatus Puniceispirillum marinum
           IMCC1322]
          Length = 254

 Score =  232 bits (592), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 122/244 (50%), Positives = 156/244 (63%), Gaps = 1/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEY+G+ + GWQRQ NG ++Q  +E+A F  TGE + V GAGRTDSGVHAL QVA
Sbjct: 4   RIFITIEYDGAPFVGWQRQDNGITVQQELEEAAFAFTGEKINVQGAGRTDSGVHALGQVA 63

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           H D+  ++ P  + +ALNA+L  +  IS+L+   V    HARFSAI R YLYRI+ R+ P
Sbjct: 64  HLDVPEKFAPNRVMEALNAHLSHT-AISVLDAYEVPDDAHARFSAIGRRYLYRILPRRQP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            AL+ GR W   + LD + M+  A  L+GRHDF +FR+  CQA S IRT+D   V     
Sbjct: 123 PALDAGRVWHHKQPLDADAMQAGADMLIGRHDFNSFRAAQCQAESSIRTLDILQVEQVSA 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + V ARSFLH Q+R+  G+L LVG GKW   D++ AL A DR   GP APP GLY  
Sbjct: 183 EIHLHVEARSFLHHQVRNIAGTLALVGTGKWQPDDVKAALAAADRSAAGPTAPPHGLYLT 242

Query: 243 SVEY 246
            V Y
Sbjct: 243 DVFY 246


>gi|310816231|ref|YP_003964195.1| tRNA pseudouridine synthase A [Ketogulonicigenium vulgare Y25]
 gi|308754966|gb|ADO42895.1| tRNA pseudouridine synthase A [Ketogulonicigenium vulgare Y25]
          Length = 255

 Score =  232 bits (591), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 112/251 (44%), Positives = 158/251 (62%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G  + GWQRQ    S+QG+IE A+  +      +  AGRTD+GVH   Q
Sbjct: 1   MPRYALLVEYDGRPFSGWQRQSELPSVQGAIEAALAKLEPRDHTIAAAGRTDTGVHGTGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ ++W P  L +ALN +L+ +  ++IL  + V   +HARFSA  R Y++R+++R+
Sbjct: 61  VAHCDMDKDWDPFRLSEALNHHLRPA-PVAILRAARVADDWHARFSAYERRYIFRLLSRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL +E G+ W +  +LD + MR  A HL+G HDFTTFRS  CQA SP++TID   +   
Sbjct: 120 APLTVENGQFWRVGHALDADLMRAGAAHLIGLHDFTTFRSSICQAKSPVKTIDEISITEI 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      + ARSFLH Q+RS VG+L+ VG G W    + + L A+DR  CGP+ PP
Sbjct: 180 PRHDGTEFRFFLRARSFLHNQVRSIVGTLERVGAGAWPPEKVAEVLAARDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   VEY 
Sbjct: 240 QGLYLAGVEYP 250


>gi|170749553|ref|YP_001755813.1| tRNA pseudouridine synthase A [Methylobacterium radiotolerans JCM
           2831]
 gi|238688894|sp|B1M6N9|TRUA_METRJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|170656075|gb|ACB25130.1| tRNA pseudouridine synthase A [Methylobacterium radiotolerans JCM
           2831]
          Length = 253

 Score =  231 bits (590), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 115/250 (46%), Positives = 160/250 (64%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY+GS + GWQRQ +  ++QG+IE A+   +GE   +  AGRTD+GVHA+ Q
Sbjct: 1   MPRYKLVIEYDGSPFCGWQRQADDPTVQGAIEAAVTRFSGENARLTCAGRTDAGVHAIHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W    +  ALNA+L+    ++IL+   V   F AR SAIRR Y YRI+ R+
Sbjct: 61  VAHLDLAKDWRTDTVRDALNAHLR-PQPVAILSAETVPDSFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           +P AL +   W +P  LD + M  AAQ LVGRHDF+ FR+  CQA+SPIRT++  DV   
Sbjct: 120 SPAALTRAHVWHVPWPLDADLMHDAAQRLVGRHDFSAFRAAECQANSPIRTLEQLDVARA 179

Query: 179 --SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             +  + I +   ARSFLH Q+R+ VG+L L G  +  + D+ + L + D+  CGPLAP 
Sbjct: 180 PMALHDEIVVATAARSFLHHQVRAMVGTLMLAGCRRLAADDVAEILASGDKSRCGPLAPA 239

Query: 237 EGLYFDSVEY 246
            GL F  V+Y
Sbjct: 240 AGLTFVGVDY 249


>gi|126731534|ref|ZP_01747340.1| tRNA pseudouridine synthase A [Sagittula stellata E-37]
 gi|126708070|gb|EBA07130.1| tRNA pseudouridine synthase A [Sagittula stellata E-37]
          Length = 249

 Score =  231 bits (590), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 113/244 (46%), Positives = 156/244 (63%), Gaps = 5/244 (2%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           +EY+G  + GWQRQ    S+Q +IE A+  +      + GAGRTD+GVHA  QVA  D+ 
Sbjct: 1   MEYDGRPFSGWQRQAAQPSVQQAIEDALARLEPGPFTIAGAGRTDAGVHARGQVAQCDMA 60

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
           ++W P  L +ALN +LK +  ++I   + V   +HARFSA+ R YL+RI+ R+AP  LE+
Sbjct: 61  KDWDPFRLSEALNFHLKPA-PVAIRACARVADDWHARFSAVERRYLFRILMRRAPATLEE 119

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF----GNL 183
           G+ W +   LD   MR  A HLVGRHDFTTFRS+ CQA SP++T+D  ++ +     G  
Sbjct: 120 GQVWRVMHPLDVTAMREGAAHLVGRHDFTTFRSVMCQAKSPVKTLDSLEIKAVDGPAGPE 179

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           +   + ARSFLH Q+RSFVG+L+ VG G W    +  AL+A+DR  CGP+ PP+GLY   
Sbjct: 180 VWFSLRARSFLHNQVRSFVGTLERVGAGAWAPDRVGAALEARDRAACGPVCPPQGLYLTG 239

Query: 244 VEYS 247
           V Y 
Sbjct: 240 VGYP 243


>gi|306840229|ref|ZP_07473004.1| tRNA pseudouridine synthase A [Brucella sp. BO2]
 gi|306289834|gb|EFM61013.1| tRNA pseudouridine synthase A [Brucella sp. BO2]
          Length = 207

 Score =  231 bits (588), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 112/202 (55%), Positives = 143/202 (70%), Gaps = 1/202 (0%)

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARF 105
            AGRTD+GVHA  QVAH DL ++W    +  A+NA+L ++D  ISILN+      F ARF
Sbjct: 3   AAGRTDAGVHATAQVAHVDLAKDWGAGKVRDAVNAHLVMADERISILNVEKTTDTFDARF 62

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           SA  R YLYRI  R+APLA++  RAW + K LD + M  AAQ L+G HDFTTFR+  CQA
Sbjct: 63  SARARHYLYRIHNRRAPLAVDYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQCQA 122

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            SP++T+D  DV   G++IE+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+A+
Sbjct: 123 KSPVKTLDRLDVTRNGDMIEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALEAR 182

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           DRK CG +APP GLY   V+Y+
Sbjct: 183 DRKACGQVAPPYGLYLVGVDYA 204


>gi|189023111|ref|YP_001932852.1| tRNA pseudouridine synthase A [Brucella abortus S19]
 gi|189021685|gb|ACD74406.1| tRNA pseudouridine synthase [Brucella abortus S19]
          Length = 207

 Score =  230 bits (586), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 111/202 (54%), Positives = 143/202 (70%), Gaps = 1/202 (0%)

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARF 105
            AGRTD+GVHA  QVAH DL ++W    +  A+NA+L ++D  ISILN+      F ARF
Sbjct: 3   AAGRTDAGVHATAQVAHVDLAKDWGAGKVRDAVNAHLVMADERISILNVEKTTDTFDARF 62

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           SA  R YLYRI  R+APLA++  RAW + K LD + M  AAQ L+G HDFTTFR+  CQA
Sbjct: 63  SARARHYLYRIHNRRAPLAVDYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQCQA 122

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            SP++T+D  DV   G+++E+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+A+
Sbjct: 123 KSPVKTLDRLDVTRNGDMVEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALEAR 182

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           DRK CG +APP GLY   V+Y+
Sbjct: 183 DRKACGQVAPPYGLYLVGVDYA 204


>gi|255264700|ref|ZP_05344042.1| tRNA pseudouridine synthase A [Thalassiobium sp. R2A62]
 gi|255107035|gb|EET49709.1| tRNA pseudouridine synthase A [Thalassiobium sp. R2A62]
          Length = 257

 Score =  229 bits (584), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 117/250 (46%), Positives = 163/250 (65%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQK+  S+QG+IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRYALKIEYDGAPFAGWQRQKDQPSVQGAIEAALAKLEPRAHTIAAAGRTDAGVHGLAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R W    L +ALN +LK +  ++I++ +IV+  +HARFSA+ R YL+R++ R+
Sbjct: 61  VAHCDLERGWQAFRLSEALNYHLKPA-PVAIVDCAIVEGDWHARFSAVERRYLFRLVARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A +   +GR W +   LD   M+ AA HLVG HDFTTFRS  CQ++SP++T+D  D++  
Sbjct: 120 ASMTHLRGRVWHVQNPLDVAAMQAAAAHLVGLHDFTTFRSSICQSASPVKTLDRLDISEH 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      V ARSFLH Q+RSFVG+L+ VG G W    +  AL+A +R  CGP++PP
Sbjct: 180 ETNAGVEYRFDVRARSFLHNQVRSFVGTLERVGAGSWDPDRVRVALEACERSTCGPVSPP 239

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 240 QGLYLAGVGY 249


>gi|209965580|ref|YP_002298495.1| tRNA pseudouridine synthase A [Rhodospirillum centenum SW]
 gi|238057735|sp|B6IPI0|TRUA_RHOCS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|209959046|gb|ACI99682.1| tRNA pseudouridine synthase A [Rhodospirillum centenum SW]
          Length = 245

 Score =  229 bits (584), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 121/246 (49%), Positives = 161/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ + +EY+G  + GWQRQ NG S+Q ++E+AI+  T E V V  AGRTD+GVHAL  
Sbjct: 1   MQRWKLTLEYDGRPFVGWQRQDNGPSVQQALEEAIYRFTQETVTVFCAGRTDAGVHALAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA  DL RE     +  ALN +LK    +++L +  V   FHARFS + R+YLYRI+ R+
Sbjct: 61  VASVDLAREATADKVQAALNFHLK-PHPVAVLRVEPVAPDFHARFSCLGRAYLYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP ALE GR W +   LD E M  AAQ LVG+HDF++FR+  CQA SP++T+    V   
Sbjct: 120 APAALEAGRVWHVQGGLDAEAMHEAAQRLVGQHDFSSFRASLCQAKSPVKTLSDLSVARV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I   ARSFLH Q+R+ VG+LKLVG+G+WT+ D+ +AL A++R   GP AP  GLY
Sbjct: 180 GEEVRIVARARSFLHHQVRNMVGTLKLVGEGRWTADDVSRALAARNRSAAGPTAPAAGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FTEAWY 245


>gi|306838494|ref|ZP_07471334.1| tRNA pseudouridine synthase A [Brucella sp. NF 2653]
 gi|306406426|gb|EFM62665.1| tRNA pseudouridine synthase A [Brucella sp. NF 2653]
          Length = 207

 Score =  229 bits (584), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 111/202 (54%), Positives = 142/202 (70%), Gaps = 1/202 (0%)

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARF 105
            AGRTD+GVHA  QVAH DL ++W    +  A+NA+L ++D  ISILN+      F ARF
Sbjct: 3   AAGRTDAGVHATAQVAHVDLAKDWGAGKVRDAVNAHLVMADERISILNVEKTTDTFDARF 62

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           SA  R YLYRI  R+APLA+   RAW + K LD + M  AAQ L+G HDFTTFR+  CQA
Sbjct: 63  SARARHYLYRIHNRRAPLAVNYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQCQA 122

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            SP++T+D  DV   G+++E+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+A+
Sbjct: 123 KSPVKTLDRLDVTRNGDMVEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALEAR 182

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           DRK CG +APP GLY   V+Y+
Sbjct: 183 DRKACGQVAPPYGLYLVGVDYA 204


>gi|304320576|ref|YP_003854219.1| tRNA pseudouridine synthase A [Parvularcula bermudensis HTCC2503]
 gi|303299478|gb|ADM09077.1| tRNA pseudouridine synthase A [Parvularcula bermudensis HTCC2503]
          Length = 253

 Score =  229 bits (584), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 113/245 (46%), Positives = 153/245 (62%), Gaps = 1/245 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + +E++G+ + GWQRQ NG S+QG+IE+A   +T      +GAGRTDSGVHA+   A
Sbjct: 6   RYRIEVEFDGTPFVGWQRQDNGPSVQGAIEEAAARLTQAPGACYGAGRTDSGVHAIAMTA 65

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           H DL +   P  +   LNAYL+ +  +SIL    V   FHARF   RR YLYR++ R++P
Sbjct: 66  HLDLAKALPPDNVRDGLNAYLRPA-PVSILLAQPVSPDFHARFQCHRRHYLYRLLDRRSP 124

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             L + R W +   LD + M  AA  L+G+HDFTT+RS HCQA SP++T+  F+V   G 
Sbjct: 125 PVLMRDRVWHVIAPLDVDAMAKAAHPLIGQHDFTTYRSAHCQAESPLKTLSQFEVTRVGQ 184

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +   + A SFLH Q+RS VG+L  VG G+   +    ALQA DR+ CGP+AP  GLYF 
Sbjct: 185 EVHCALSAPSFLHNQVRSLVGTLVQVGLGRAALSQPYDALQACDRRACGPVAPAHGLYFV 244

Query: 243 SVEYS 247
             +Y 
Sbjct: 245 KADYP 249


>gi|330813516|ref|YP_004357755.1| tRNA pseudouridine synthase A [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327486611|gb|AEA81016.1| tRNA pseudouridine synthase A [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 245

 Score =  228 bits (582), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 117/246 (47%), Positives = 160/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  I+EY+G+ + GWQRQ NG S+Q ++EK++  +T E + +HG+GRTD+GVHA  Q
Sbjct: 1   MRRYKCIVEYDGTSFVGWQRQTNGYSVQEAVEKSLKSITQEKIRIHGSGRTDTGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD         +  ALN YLK  + ISIL+  IVD  F AR SAI R+Y Y II R 
Sbjct: 61  VIHFDSNTNLDEYTITSALNHYLK-KELISILSTEIVDDNFDARRSAILRTYEYLIINRA 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APLA++K +AW I K L+ + +  A +   G HDFTTFR+  C+ASSPIRTI++ +  + 
Sbjct: 120 APLAIDKNKAWHISKPLNEKLIFAAIKIFEGTHDFTTFRAASCEASSPIRTIEYTEAFAR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I   ++SFL  Q+RS +G+LKL+G+ KW+  DL+ AL ++DR  C  LAP  GLY
Sbjct: 180 NEEILITFQSKSFLQHQVRSMIGALKLIGEEKWSIRDLQSALDSKDRSRCAALAPACGLY 239

Query: 241 FDSVEY 246
              V +
Sbjct: 240 LLKVSF 245


>gi|119383286|ref|YP_914342.1| tRNA pseudouridine synthase A [Paracoccus denitrificans PD1222]
 gi|166228744|sp|A1AZF2|TRUA_PARDP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119373053|gb|ABL68646.1| tRNA pseudouridine synthase A [Paracoccus denitrificans PD1222]
          Length = 261

 Score =  228 bits (580), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 116/253 (45%), Positives = 155/253 (61%), Gaps = 8/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGR---TDSGVHA 57
           M R+ ++IEY+GS + GWQ Q    S+Q +IE A+  +               TD+GVHA
Sbjct: 1   MPRFALLIEYDGSPFAGWQAQAERPSVQSTIEAALGRLDPGFAAGARIAAAGRTDAGVHA 60

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
             QVAH DL R+W P  L +ALN +LK +  ++IL  + V   FHARFSA  R YL+R++
Sbjct: 61  TGQVAHADLARDWDPFRLSEALNWHLKPA-PVAILAAARVADDFHARFSAHERRYLFRLV 119

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R+APL  ++GRAW +P  LD   MR  A HL+GRHDFTTFRS  CQA+SP++T+D   +
Sbjct: 120 ARRAPLTHDRGRAWQVPHRLDLAAMRAGAAHLLGRHDFTTFRSTMCQANSPVKTLDELTI 179

Query: 178 NSF----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
           +      G      + ARSFLH Q+RS VG+L+ VG G W    + +AL A DR  CGP+
Sbjct: 180 DEAEIPQGREYRFFLRARSFLHNQVRSIVGTLERVGAGAWPPGRVAEALAACDRAACGPV 239

Query: 234 APPEGLYFDSVEY 246
            PP+GLY   V Y
Sbjct: 240 CPPQGLYLTGVGY 252


>gi|302384321|ref|YP_003820144.1| tRNA pseudouridine synthase A [Brevundimonas subvibrioides ATCC
           15264]
 gi|302194949|gb|ADL02521.1| tRNA pseudouridine synthase A [Brevundimonas subvibrioides ATCC
           15264]
          Length = 247

 Score =  228 bits (580), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 109/246 (44%), Positives = 155/246 (63%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY+G  Y G+Q Q    ++QG +E A+    G+ V +  AGRTDSGVHA  Q
Sbjct: 1   MPRYRLTLEYDGRPYAGFQAQDGLPTVQGVVETAVTAFCGQTVRIAAAGRTDSGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL + W    +  ALNA++ + + +++L    V   +HARFSA  R YLYRI+ R 
Sbjct: 61  VAHVDLDKAWPASTVMNALNAHM-VREGVAVLACEAVPDDWHARFSATGRRYLYRILNRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              ALE+G+ W + + LD   M+  A HL+G HDFTTFR + CQ+ SP +T+D   V++ 
Sbjct: 120 GRPALERGKVWHVRRPLDVAAMQAGADHLIGHHDFTTFRDLACQSKSPEKTLDVARVSAV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + +   ARSFLH Q+RS  G+L  VG G+W+  D++ AL+A+DR  CGP++P +GLY
Sbjct: 180 GEEVHLVFEARSFLHRQVRSMTGTLVEVGLGRWSPDDVKTALEARDRTACGPVSPSDGLY 239

Query: 241 FDSVEY 246
              V Y
Sbjct: 240 LTGVAY 245


>gi|306846234|ref|ZP_07478796.1| tRNA pseudouridine synthase A [Brucella sp. BO1]
 gi|306273485|gb|EFM55346.1| tRNA pseudouridine synthase A [Brucella sp. BO1]
          Length = 207

 Score =  227 bits (579), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 110/202 (54%), Positives = 142/202 (70%), Gaps = 1/202 (0%)

Query: 47  GAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDT-ISILNLSIVDKQFHARF 105
            AGRTD+GVHA  QVAH DL ++W    +  A+NA+L +++  ISILN+      F ARF
Sbjct: 3   AAGRTDAGVHATAQVAHVDLAKDWGAGKVRDAVNAHLVMAEERISILNVEKTTDTFDARF 62

Query: 106 SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA 165
           SA  R YLYRI  R+APLA+   RAW + K LD + M  AAQ L+G HDFTTFR+  CQA
Sbjct: 63  SARARHYLYRIHNRRAPLAVNYQRAWWVQKQLDADAMHEAAQRLLGEHDFTTFRATQCQA 122

Query: 166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQ 225
            SP++T+D  DV   G+++E+RV ARSFLH Q+RSF GSL  VG G+WT+ DL+ AL+A+
Sbjct: 123 KSPVKTLDRLDVTRNGDMVEMRVSARSFLHNQVRSFAGSLMEVGVGRWTADDLQAALEAR 182

Query: 226 DRKECGPLAPPEGLYFDSVEYS 247
           DRK CG +APP GLY   V+Y+
Sbjct: 183 DRKACGQVAPPYGLYLIGVDYA 204


>gi|73667044|ref|YP_303060.1| tRNA pseudouridine synthase A [Ehrlichia canis str. Jake]
 gi|123773369|sp|Q3YS43|TRUA_EHRCJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|72394185|gb|AAZ68462.1| tRNA pseudouridine synthase [Ehrlichia canis str. Jake]
          Length = 245

 Score =  226 bits (577), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 114/246 (46%), Positives = 159/246 (64%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + IEYNGS + GWQRQK+  +SIQ  +E+AIF  + E V  + AGRTD+GVHAL Q
Sbjct: 1   MRYKITIEYNGSNFIGWQRQKHLSNSIQEILEEAIFKFSRESVTTYVAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL  ++   ++  A+N +L I  +IS+LN+   D +FHARFSA +R YLY+II R 
Sbjct: 61  VAHFDLTADFDAYVVRNAINYHL-IPHSISVLNVEKTDDEFHARFSAKKRHYLYKIINRY 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +PL ++  RAWL+   LD E M  A +++ G HDF++FR+ HCQ+ SP++T+D   +   
Sbjct: 120 SPLTIDYNRAWLVRNPLDVEKMMRAVEYIKGNHDFSSFRARHCQSKSPVKTMDDLKIIHS 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I+I   A SFLH Q+R  VG+L   G   +     +  L+A+DR   G  APP GLY
Sbjct: 180 DQCIDIYFSAISFLHNQVRIIVGTLVECGKNSFPPEYTKDILEAKDRSYAGMTAPPYGLY 239

Query: 241 FDSVEY 246
           F  V+Y
Sbjct: 240 FVKVDY 245


>gi|158422420|ref|YP_001523712.1| tRNA pseudouridine synthase A [Azorhizobium caulinodans ORS 571]
 gi|172048047|sp|A8IQL3|TRUA_AZOC5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|158329309|dbj|BAF86794.1| tRNA pseudouridine synthase [Azorhizobium caulinodans ORS 571]
          Length = 258

 Score =  226 bits (577), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 120/246 (48%), Positives = 162/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQ Q    ++QG +  A+   +GE   V GAGRTD+GVHA  Q
Sbjct: 1   MPRYKLTIEYDGTPFAGWQIQAELPTVQGVLAAAVKGFSGEEAHVAGAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH  L R+W P  +  A+ A+L+      +    + D  F ARFSA++R YLYRI+ R+
Sbjct: 61  VAHIHLARDWRPDQVRDAMTAHLRPHPVAVVAVERVAD-DFDARFSAVKRHYLYRIVNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             LAL++ RAW +P+ LD   M +AAQ L+G+HDFTTFR+  CQA+SP +T+D  DV   
Sbjct: 120 PDLALDRDRAWRVPQKLDASAMHVAAQRLLGKHDFTTFRAAECQAASPEKTLDQLDVMRS 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I   ARSFLH Q+RS VGSL  VG+G+W++ DL  AL A+DR+ CGP+AP  GLY
Sbjct: 180 GDDIRIVTSARSFLHHQVRSMVGSLIRVGEGRWSADDLADALAARDRRRCGPMAPACGLY 239

Query: 241 FDSVEY 246
             +V Y
Sbjct: 240 LAAVSY 245


>gi|329890848|ref|ZP_08269191.1| tRNA pseudouridine synthase A [Brevundimonas diminuta ATCC 11568]
 gi|328846149|gb|EGF95713.1| tRNA pseudouridine synthase A [Brevundimonas diminuta ATCC 11568]
          Length = 249

 Score =  226 bits (576), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 116/246 (47%), Positives = 157/246 (63%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY   +EY+GS Y G+Q Q    ++QG+IE AI   +G+ V +  AGRTD+GVHA  Q
Sbjct: 1   MPRYRFTVEYDGSAYNGFQAQLGQPTVQGAIETAITAFSGQAVRIAAAGRTDTGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
             H DL R+W    +  ALNA+L + + +++L+ + V   +HARF+A  R YLYRI+ R 
Sbjct: 61  TCHVDLERDWPAQTVMNALNAHL-VKEAVAVLDCTPVSDDWHARFTANGRKYLYRILNRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL++GR W + K LD E M  AAQ L+G HDFTTFR   CQ++SPI+T+D   V+  
Sbjct: 120 GRPALDRGRVWHVRKPLDAEAMHAAAQALIGLHDFTTFRDAACQSASPIKTLDVARVSRV 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + +   ARSFLH Q+RS  GS+  VG G+W   DL  AL+A+DR  CGP+AP +GLY
Sbjct: 180 GEEVHLVFEARSFLHRQVRSMAGSIAEVGLGRWRPADLADALEARDRARCGPVAPSDGLY 239

Query: 241 FDSVEY 246
              V Y
Sbjct: 240 LTGVTY 245


>gi|94495734|ref|ZP_01302314.1| tRNA pseudouridine synthase A [Sphingomonas sp. SKA58]
 gi|94425122|gb|EAT10143.1| tRNA pseudouridine synthase A [Sphingomonas sp. SKA58]
          Length = 246

 Score =  226 bits (576), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 124/246 (50%), Positives = 160/246 (65%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+   +E++G  + GWQRQ +G S+Q +IE AI  VTGE  V+H AGRTD+GVH L  
Sbjct: 1   MPRFAFTVEFDGRPFMGWQRQAHGPSVQQTIEDAIAAVTGEAAVIHAAGRTDAGVHGLAM 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            AH D+ +   P  L +A+NA ++ +  ++IL    V   +HARFS   RSY+YRI  R+
Sbjct: 61  RAHADIAKNIAPFRLMEAINARMRPA-PVAILACETVADDWHARFSCTGRSYVYRIANRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           APL  + G  W + + LD + M+ AAQHLVGRHDFTTFRS HCQA SP++T+D  DV   
Sbjct: 120 APLTFDAGLVWRVVQPLDADAMQAAAQHLVGRHDFTTFRSAHCQAHSPLKTLDRLDVERQ 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I   ARSFLH Q+RS VG L +VG G WT+ DL  AL A+DR   G  APP+GLY
Sbjct: 180 GDRIAIHAAARSFLHHQVRSMVGCLAMVGMGHWTANDLRDALAARDRAALGLNAPPDGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FVRATY 245


>gi|57239154|ref|YP_180290.1| tRNA pseudouridine synthase A [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58579105|ref|YP_197317.1| tRNA pseudouridine synthase A [Ehrlichia ruminantium str.
           Welgevonden]
 gi|62901163|sp|Q5HBA4|TRUA_EHRRW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|57161233|emb|CAH58149.1| tRNA pseudouridine synthase A [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58417731|emb|CAI26935.1| tRNA pseudouridine synthase A [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 246

 Score =  224 bits (571), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 111/247 (44%), Positives = 164/247 (66%), Gaps = 2/247 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY ++IEY+GS + GWQ+Q  N +SIQ  +EKAIF  + + V+V+GAGRTD+GVHAL Q
Sbjct: 1   MRYKIVIEYDGSDFIGWQKQNHNSNSIQEILEKAIFKFSKQHVIVYGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL  ++   I+  A+N +L IS  I+++++   D  FHARFSA RR YLY+I+ R 
Sbjct: 61  VAHFDLTTDFETYIVRNAINYHL-ISHAIAVVHVEKTDTDFHARFSAKRRYYLYKIVNRY 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +PL +++ RAWL+   L+ ENM  A  ++ G H+F++FR+  CQ+ SPI+T+D+  +   
Sbjct: 120 SPLTIDRNRAWLVHTPLNVENMIKAVCYIKGNHNFSSFRAKCCQSKSPIKTVDNLSITYN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I+I + A SFLH Q+R  VG+L   G G +    ++  ++A +R   G  AP  GLY
Sbjct: 180 HPYIDINISAISFLHHQVRIIVGTLVECGKGYFPPEHIKTIMEANNRSYAGTTAPSYGLY 239

Query: 241 FDSVEYS 247
           F  V+YS
Sbjct: 240 FVKVDYS 246


>gi|58617163|ref|YP_196362.1| tRNA pseudouridine synthase A [Ehrlichia ruminantium str. Gardel]
 gi|62901148|sp|Q5FGS1|TRUA_EHRRG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|58416775|emb|CAI27888.1| tRNA pseudouridine synthase A [Ehrlichia ruminantium str. Gardel]
          Length = 246

 Score =  223 bits (569), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 110/247 (44%), Positives = 163/247 (65%), Gaps = 2/247 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY ++IEY+GS + GWQ+Q  N +SIQ  +EKAIF  + + V V+GAGRTD+GVHAL Q
Sbjct: 1   MRYKIVIEYDGSNFIGWQKQNHNSNSIQEILEKAIFKFSKQHVTVYGAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL  ++   I+  A+N +L IS  I+++++   D  FHARFSA RR YLY+I+ R 
Sbjct: 61  VAHFDLTTDFETYIVRNAINYHL-ISHAIAVVHVEKTDTDFHARFSAKRRYYLYKIVNRY 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +PL +++ RAWL+   L+ ENM  A  ++ G H+F++FR+  CQ+ SP++T+D+  +   
Sbjct: 120 SPLTIDRNRAWLVHTPLNVENMIKAVCYIKGNHNFSSFRAKCCQSKSPVKTVDNLSITYN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I+I + A SFLH Q+R  VG+L   G G +    ++  ++A +R   G  AP  GLY
Sbjct: 180 HPYIDINISAISFLHHQVRIIVGTLVECGKGYFPPEHIKTIMEANNRSYAGTTAPSYGLY 239

Query: 241 FDSVEYS 247
           F  V+YS
Sbjct: 240 FVKVDYS 246


>gi|188580854|ref|YP_001924299.1| tRNA pseudouridine synthase A [Methylobacterium populi BJ001]
 gi|238692887|sp|B1ZGA6|TRUA_METPB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|179344352|gb|ACB79764.1| tRNA pseudouridine synthase A [Methylobacterium populi BJ001]
          Length = 252

 Score =  223 bits (568), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 112/250 (44%), Positives = 158/250 (63%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY+G  + GWQRQ +  ++Q +IE A+   +GE   +  AGRTD+GVHA+ Q
Sbjct: 1   MPRYKLVIEYDGGPFCGWQRQADDPTVQAAIETAVTRFSGETARLTCAGRTDAGVHAIHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R+W    +  ALNA+L+    I+I++  +V   F AR SAIRR Y YRI+ R+
Sbjct: 61  VAHLDLARDWRTDTVRDALNAHLR-PQPIAIVSAEVVTHDFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           +P AL +   W +P  LD + M  AAQ L+GRHDF+ FR+  CQA+SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWHVPWPLDADLMHAAAQRLLGRHDFSAFRAAECQAASPVRTLEQLDVTRQ 179

Query: 179 SFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             G   EI +   ARSFLH Q+R+  G+L L G  + ++ D+ + L  + +  CGPLAP 
Sbjct: 180 RMGLFEEIVIATSARSFLHHQVRAMAGTLMLAGCRRLSADDVAEILATKAKHRCGPLAPA 239

Query: 237 EGLYFDSVEY 246
            GL F  V+Y
Sbjct: 240 CGLTFVGVDY 249


>gi|58584685|ref|YP_198258.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont strain TRS of
           Brugia malayi]
 gi|58419001|gb|AAW71016.1| Pseudouridylate synthase (tRNA psi55) [Wolbachia endosymbiont
           strain TRS of Brugia malayi]
          Length = 249

 Score =  223 bits (567), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 117/246 (47%), Positives = 156/246 (63%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + IEYNGS + GWQ+Q++  +SIQ +IE AIF  +GE V +H  GRTD+GVHAL Q
Sbjct: 5   VRYKITIEYNGSSFSGWQKQQHSANSIQETIENAIFNFSGEKVTLHCGGRTDAGVHALGQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+ R++    +  A+N +LK S  I +LN   VD  FH+RFSA +R Y YRII R 
Sbjct: 65  VAHFDMERKFELYKIRNAINYHLK-SIPIVVLNAETVDNTFHSRFSAKKRYYEYRIINRY 123

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP ALE G AW +   LD   MR AA++L+G+H+  +FRS  CQA++PIRTID  D+   
Sbjct: 124 APAALEAGYAWQVFNPLDVNIMREAAKYLLGKHNLLSFRSKDCQATNPIRTIDDIDIVQN 183

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I++ A SFLH Q+R  VG+L   G  +     +   L    R   G  APP GLY
Sbjct: 184 GSHIYIKISAISFLHNQVRIIVGTLVEFGKSRTNPQKMLNILNQCKRNAAGVTAPPFGLY 243

Query: 241 FDSVEY 246
              ++Y
Sbjct: 244 LAKIDY 249


>gi|218529891|ref|YP_002420707.1| tRNA pseudouridine synthase A [Methylobacterium chloromethanicum
           CM4]
 gi|254789640|sp|B7KVW3|TRUA_METC4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|218522194|gb|ACK82779.1| tRNA pseudouridine synthase A [Methylobacterium chloromethanicum
           CM4]
          Length = 250

 Score =  223 bits (567), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 112/250 (44%), Positives = 158/250 (63%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY+G+ + GWQRQ +  ++Q +IE A+   +GE   +  AGRTD+GVHA+ Q
Sbjct: 1   MPRYKLVIEYDGAPFRGWQRQADDPTVQAAIETAVTRFSGETARLTCAGRTDAGVHAIHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W    +  ALNA+L+    +SIL+  +V ++F AR SAIRR Y YRI+ R+
Sbjct: 61  VAHLDLAKDWRTDTVRDALNAHLR-PQPVSILSAEVVPQEFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           +P AL +   W +P  LD E M  AAQ L+G HDF+ FR+  CQA SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWQVPWPLDAELMHRAAQRLLGHHDFSAFRAAECQAKSPMRTLEQLDVTRE 179

Query: 179 SFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             G   EI +   ARSFLH Q+R+  G+L L G  + ++ D+ + L    +  CGPLAP 
Sbjct: 180 RMGLFEEIVIATSARSFLHHQVRAMAGTLMLAGCKRLSADDVAEILATGAKHRCGPLAPA 239

Query: 237 EGLYFDSVEY 246
            GL F  V+Y
Sbjct: 240 CGLTFVGVDY 249


>gi|254560755|ref|YP_003067850.1| tRNA pseudouridine synthase A [Methylobacterium extorquens DM4]
 gi|254268033|emb|CAX23904.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Methylobacterium extorquens
           DM4]
          Length = 250

 Score =  222 bits (566), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 111/251 (44%), Positives = 159/251 (63%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY+G+ + GWQRQ +  ++Q +IE A+   +GE   +  AGRTD+GVHA+ Q
Sbjct: 1   MPRYKLVIEYDGAPFRGWQRQADDPTVQAAIETAVTRFSGETARLTCAGRTDAGVHAIHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W    +  ALNA+L+    ++IL+  +V ++F AR SAIRR Y YRI+ R+
Sbjct: 61  VAHLDLAKDWRTDTVRDALNAHLR-PQPVAILSAEVVPQEFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           +P AL +   W +P  LD E M  AAQ L+G HDF+ FR+  CQA SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWQVPWPLDAELMHRAAQRLLGHHDFSAFRAAECQAKSPMRTLEQLDVTRV 179

Query: 179 SFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             G   EI +   ARSFLH Q+R+  G+L L G  + ++ D+ + L    +  CGPLAP 
Sbjct: 180 RMGLFEEIVIATSARSFLHHQVRAMAGTLMLAGCNRLSADDVAEILATGAKHRCGPLAPA 239

Query: 237 EGLYFDSVEYS 247
            GL F  V+Y+
Sbjct: 240 CGLTFVGVDYA 250


>gi|126725547|ref|ZP_01741389.1| tRNA pseudouridine synthase A [Rhodobacterales bacterium HTCC2150]
 gi|126704751|gb|EBA03842.1| tRNA pseudouridine synthase A [Rhodobacterales bacterium HTCC2150]
          Length = 265

 Score =  222 bits (566), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 110/251 (43%), Positives = 155/251 (61%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQ    ++QG+IE AI  +      +  AGRTD+GVHA+ Q
Sbjct: 1   MPRYALKIEYHGAPFAGWQRQPELQTVQGAIEAAIRKLEAGNAGITAAGRTDAGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ + W    L +A+N +LK    ++I+  + VD  FHARF A+ R YL+ ++ R+
Sbjct: 61  VAHVDMAKSWDLFRLTEAINHHLK-PLPVAIVACAQVDDDFHARFGALERQYLFSVVARR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +    ++G  W + + LD   M+  A HL+GRHDFTTFRS  CQA SP+RT+D   +   
Sbjct: 120 SLAVHDQGLVWQVRQPLDLARMKEGAAHLLGRHDFTTFRSTKCQADSPVRTLDELSIREI 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G   E  + ARSFLH Q+RSFVG+L+ VG G     ++ + L+A DR  CGP+APP
Sbjct: 180 ARPVGQEFEFTIRARSFLHNQVRSFVGTLEPVGAGWVHPNEVGEMLRAADRTACGPVAPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLKHVVYP 250


>gi|15604687|ref|NP_221205.1| tRNA pseudouridine synthase A [Rickettsia prowazekii str. Madrid E]
 gi|3861382|emb|CAA15281.1| PSEUDOURIDYLATE SYNTHASE I (truA) [Rickettsia prowazekii]
          Length = 253

 Score =  222 bits (566), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 112/246 (45%), Positives = 155/246 (63%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+ + GWQRQ    S+Q  +E+AI+  + E V + G+GRTD+GVHA+ Q
Sbjct: 9   MYRYKITIEYLGTHFAGWQRQAGVLSVQQILEEAIYKFSSEQVTLFGSGRTDAGVHAIGQ 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  + KA+N +++  D + + N  +V   FHARFSAI R Y+YRII R 
Sbjct: 69  VAHFDLSKYLEPYKIIKAINYFVRPYD-VGVWNCELVSNNFHARFSAISRHYIYRIINRT 127

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FRS  CQ+ SPI+T+   ++   
Sbjct: 128 YPSVIDFNRAWWISSPLDILAMQKAAAYLLGKHDFTSFRSSSCQSKSPIKTLTEINIIKE 187

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L A+DRK  GP AP  GLY
Sbjct: 188 YEEIKLYISAPSFLHYMVRNIVGSLVLVGKNIWQAEQIKNVLDARDRKIAGPTAPAFGLY 247

Query: 241 FDSVEY 246
           F   EY
Sbjct: 248 FIKAEY 253


>gi|24212681|sp|Q9ZCA3|TRUA_RICPR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|292572520|gb|ADE30435.1| tRNA pseudouridine synthase A [Rickettsia prowazekii Rp22]
          Length = 245

 Score =  222 bits (566), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 112/246 (45%), Positives = 155/246 (63%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+ + GWQRQ    S+Q  +E+AI+  + E V + G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTHFAGWQRQAGVLSVQQILEEAIYKFSSEQVTLFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  + KA+N +++  D + + N  +V   FHARFSAI R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPYKIIKAINYFVRPYD-VGVWNCELVSNNFHARFSAISRHYIYRIINRT 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FRS  CQ+ SPI+T+   ++   
Sbjct: 120 YPSVIDFNRAWWISSPLDILAMQKAAAYLLGKHDFTSFRSSSCQSKSPIKTLTEINIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L A+DRK  GP AP  GLY
Sbjct: 180 YEEIKLYISAPSFLHYMVRNIVGSLVLVGKNIWQAEQIKNVLDARDRKIAGPTAPAFGLY 239

Query: 241 FDSVEY 246
           F   EY
Sbjct: 240 FIKAEY 245


>gi|330993399|ref|ZP_08317334.1| tRNA pseudouridine synthase A [Gluconacetobacter sp. SXCC-1]
 gi|329759429|gb|EGG75938.1| tRNA pseudouridine synthase A [Gluconacetobacter sp. SXCC-1]
          Length = 275

 Score =  222 bits (565), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 119/255 (46%), Positives = 156/255 (61%), Gaps = 12/255 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHA 57
           + R+ +++EY+G G+ GWQRQK     SIQG +E A   L  G  V    AGRTD+GVHA
Sbjct: 19  VCRWAVLMEYDGRGFVGWQRQKTTGLLSIQGLLEDAATRLTNGHDVRSITAGRTDAGVHA 78

Query: 58  LRQVAHFDLVREWVPVILCKA-----LNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
             QVAH D   +   V L  A     LN Y+K    + ++   ++  Q++ARFSAI R+Y
Sbjct: 79  SGQVAHLDFPAD---VTLSSATVRDGLNFYMKPHPVVVLMARPVL-PQWNARFSAISRAY 134

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            YRI+ R A  ALE G+ W +   LD + MR AA HL+GRHDFT+FR+  CQA SP+RT+
Sbjct: 135 RYRILNRAARPALEDGQVWHVRAPLDVDGMRQAAAHLLGRHDFTSFRATACQARSPVRTL 194

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           D  DV   G  + I   ARSFLH Q+R+  G+LKLVG+G+W    +  AL A DR+  GP
Sbjct: 195 DRLDVKREGEYVVIEAAARSFLHHQVRNMAGTLKLVGEGRWEPAQVAHALAACDRRAAGP 254

Query: 233 LAPPEGLYFDSVEYS 247
            APPEGL    V Y+
Sbjct: 255 TAPPEGLCLTGVGYA 269


>gi|163747262|ref|ZP_02154617.1| tRNA pseudouridine synthase A [Oceanibulbus indolifex HEL-45]
 gi|161379537|gb|EDQ03951.1| tRNA pseudouridine synthase A [Oceanibulbus indolifex HEL-45]
          Length = 257

 Score =  222 bits (565), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 118/250 (47%), Positives = 157/250 (62%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY+G+ + GWQRQ +  ++QG IE A+  +      +  AGRTD+GVH L Q
Sbjct: 1   MPRYALKIEYHGAPFNGWQRQVDLPTVQGFIEAALARLEPGAHTIAAAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH D+ R+W P  L +ALN +LK    I+I +  +  + FHARFSA+ R Y + I++R+
Sbjct: 61  VAHCDMARDWSPFRLGEALNYHLK-PQPIAITDCVLAPEDFHARFSALERRYHFCILSRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--- 177
           AP   + G  W +   LD E M+ AA  LVG+HDFTTFRS  CQA SP++T+D  DV   
Sbjct: 120 APAVHQAGLVWQVKHRLDVEAMQAAADLLVGKHDFTTFRSTICQAVSPVKTLDRLDVREV 179

Query: 178 -NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             + G      V ARSFLH Q+RSFVG+L+ VG G W+  D+  AL A+DR  CGP+ PP
Sbjct: 180 ETATGTEYHFDVRARSFLHNQVRSFVGTLERVGAGSWSVADMGAALAAKDRAACGPVCPP 239

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 240 HGLYLAHVSY 249


>gi|260576677|ref|ZP_05844664.1| tRNA pseudouridine synthase A [Rhodobacter sp. SW2]
 gi|259021162|gb|EEW24471.1| tRNA pseudouridine synthase A [Rhodobacter sp. SW2]
          Length = 257

 Score =  222 bits (565), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 117/252 (46%), Positives = 162/252 (64%), Gaps = 6/252 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IEY+G+ + GWQRQ  G  S+Q ++E A+  +      V  AGRTD+GVHA  
Sbjct: 1   MPRYALKIEYDGTPFQGWQRQAPGQPSVQAALEAALARLQPGEHTVAAAGRTDAGVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAH DL REW    L  A+NA+L+  D +++L ++ V   FHARFSA  R YL+R++TR
Sbjct: 61  QVAHCDLDREWDTFRLAGAINAWLR-PDPVAVLAVARVADDFHARFSARERRYLFRLVTR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +AP+  ++GR W +P+ LD   MR  A HL+G+HDFTTFR+  CQA+SP++T+D   + +
Sbjct: 120 RAPVTHDRGRVWQLPQPLDAGLMRQGAAHLIGKHDFTTFRAALCQAASPVKTLDEIAIET 179

Query: 180 F----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G  I   + ARSFLH Q+RS +G+L  VG G W    + +AL A+DR  CGP+ P
Sbjct: 180 RDYPEGQEIRFTLRARSFLHNQVRSIIGTLAQVGAGHWPPERVAEALAARDRAACGPVCP 239

Query: 236 PEGLYFDSVEYS 247
           P+GLY   V Y 
Sbjct: 240 PQGLYLAGVGYP 251


>gi|240138195|ref|YP_002962667.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Methylobacterium extorquens
           AM1]
 gi|240008164|gb|ACS39390.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Methylobacterium extorquens
           AM1]
          Length = 250

 Score =  222 bits (565), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 111/250 (44%), Positives = 158/250 (63%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY+G+ + GWQRQ +  ++Q +IE A+   +GE   +  AGRTD+GVHA+ Q
Sbjct: 1   MPRYKLVIEYDGAPFRGWQRQADDPTVQAAIETAVTRFSGETARLTCAGRTDAGVHAIHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W    +  ALNA+L+    ++IL+  +V ++F AR SAIRR Y YRI+ R+
Sbjct: 61  VAHLDLAKDWRTDTVRDALNAHLR-PQPVAILSAEVVTQEFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           +P AL +   W +P  LD E M  AAQ L+G HDF+ FR+  CQA SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWQVPWPLDAELMHRAAQRLLGHHDFSAFRAAECQAKSPMRTLEQLDVTRE 179

Query: 179 SFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             G   EI +   ARSFLH Q+R+  G+L L G  + ++ D+ + L    +  CGPLAP 
Sbjct: 180 RMGLFEEIVIATSARSFLHHQVRAMAGTLMLAGCKRLSADDVAEILATGAKHRCGPLAPA 239

Query: 237 EGLYFDSVEY 246
            GL F  V+Y
Sbjct: 240 CGLTFVGVDY 249


>gi|220924613|ref|YP_002499915.1| tRNA pseudouridine synthase A [Methylobacterium nodulans ORS 2060]
 gi|254789641|sp|B8IFQ2|TRUA_METNO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219949220|gb|ACL59612.1| tRNA pseudouridine synthase A [Methylobacterium nodulans ORS 2060]
          Length = 254

 Score =  221 bits (564), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 113/246 (45%), Positives = 156/246 (63%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY +++EY+G+ + GWQRQ    ++Q ++E+AI       V VH AGRTD+GVHA  Q
Sbjct: 1   MPRYKLVVEYDGTAFAGWQRQAADRTVQQALEEAIERFVNRPVRVHCAGRTDAGVHASHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H DL REW    +  A NA+L+  + +S+L+ + V   F AR SA++R Y YRI+ R+
Sbjct: 61  VVHLDLDREWRTDTVRDATNAHLR-PEPVSVLSAARVGPDFDARHSALKRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +P AL +G  W +P +LD   M  AAQ L+GRHDF+ FR+  CQASSP+RT+D  DV   
Sbjct: 120 SPPALARGYVWHVPWALDAAAMHAAAQTLLGRHDFSAFRAAECQASSPLRTLDQLDVERR 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I +   ARSFLH Q+R  VG+L L G G+  +  +   L ++DR  CGPLAP  GL 
Sbjct: 180 GDEILVATSARSFLHHQVRGMVGTLMLAGSGRLDTAGVRAVLDSRDRARCGPLAPAAGLT 239

Query: 241 FDSVEY 246
              V+Y
Sbjct: 240 LTGVDY 245


>gi|68171651|ref|ZP_00545015.1| tRNA pseudouridine synthase [Ehrlichia chaffeensis str. Sapulpa]
 gi|88658037|ref|YP_507432.1| tRNA pseudouridine synthase A [Ehrlichia chaffeensis str. Arkansas]
 gi|123750061|sp|Q2GGK1|TRUA_EHRCR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|67998925|gb|EAM85612.1| tRNA pseudouridine synthase [Ehrlichia chaffeensis str. Sapulpa]
 gi|88599494|gb|ABD44963.1| tRNA pseudouridine synthase A [Ehrlichia chaffeensis str. Arkansas]
          Length = 245

 Score =  220 bits (561), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 112/246 (45%), Positives = 157/246 (63%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + IEYNGS + GWQ+QK+ S SIQ  +E AI   + +   V+ AGRTD+GVHAL Q
Sbjct: 1   MRYKITIEYNGSNFIGWQKQKHSSNSIQEILENAILKFSQQHTTVYVAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL       ++  A+N +L I   I+IL++   D +FHARFSA +R YLY+II R 
Sbjct: 61  VAHFDLTTNLDTYVVRNAINYHL-IPHAIAILSVEKTDDKFHARFSAKKRHYLYKIINRY 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +PL ++  RAWLI   L+ ENM  A +++ G HDF++FR+ HCQ+ +PI+TID   +   
Sbjct: 120 SPLTIDYNRAWLIHNPLNIENMIQAIEYIKGNHDFSSFRARHCQSKNPIKTIDDLKIIHN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I I + A SFLH Q+R  VG+L   G   ++   ++  L+A++R   G  APP GLY
Sbjct: 180 NQSINIHISAISFLHHQVRIIVGTLVECGKNNFSPEHIKNILKAKNRSYAGMTAPPYGLY 239

Query: 241 FDSVEY 246
           F  V+Y
Sbjct: 240 FVKVDY 245


>gi|163851061|ref|YP_001639104.1| tRNA pseudouridine synthase A [Methylobacterium extorquens PA1]
 gi|238687375|sp|A9W377|TRUA_METEP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|163662666|gb|ABY30033.1| tRNA pseudouridine synthase A [Methylobacterium extorquens PA1]
          Length = 250

 Score =  220 bits (560), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 111/250 (44%), Positives = 157/250 (62%), Gaps = 5/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY+G+ + GWQRQ +  ++Q +IE A+   +GE   +  AGRTD+GVHA+ Q
Sbjct: 1   MPRYKLVIEYDGAPFRGWQRQADDPTVQAAIETAVTRFSGETARLTCAGRTDAGVHAIHQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W    +  ALNA L+    ++IL+  +V ++F AR SAIRR Y YRI+ R+
Sbjct: 61  VAHLDLAKDWRTDTVRDALNARLR-PQPVAILSAEVVPQEFDARHSAIRRHYRYRILNRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-- 178
           +P AL +   W +P  LD E M  AAQ L+G HDF+ FR+  CQA SP+RT++  DV   
Sbjct: 120 SPAALTRAHVWQVPWPLDAELMHRAAQRLLGHHDFSAFRAAECQAKSPMRTLEQLDVTRV 179

Query: 179 SFGNLIEIRVV--ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
             G   EI +   ARSFLH Q+R+  G+L L G  + ++ D+ + L    +  CGPLAP 
Sbjct: 180 RMGLFEEIVIATSARSFLHHQVRAMAGTLMLAGCKRLSADDVAEILATGAKHRCGPLAPA 239

Query: 237 EGLYFDSVEY 246
            GL F  V+Y
Sbjct: 240 CGLTFVGVDY 249


>gi|67459748|ref|YP_247372.1| tRNA pseudouridine synthase A [Rickettsia felis URRWXCal2]
 gi|75535862|sp|Q4UJT2|TRUA_RICFE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|67005281|gb|AAY62207.1| tRNA pseudouridine synthase A [Rickettsia felis URRWXCal2]
          Length = 245

 Score =  220 bits (560), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 109/246 (44%), Positives = 151/246 (61%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQRQ    S+Q  +E+AI+  +GE V++ G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTNLAGWQRQAGVISVQQILEEAIYKFSGEQVILFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  +  A+N Y      + + N  +    FHARFSA  R Y+YRII R 
Sbjct: 61  VAHFDLSKHLEPHKIITAIN-YFARPYAVGVWNCELASNNFHARFSATSRHYIYRIINRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FR+  CQ+ SPI+T+   ++   
Sbjct: 120 YPSVIDLNRAWWISSPLDVLTMQKAAAYLLGKHDFTSFRASSCQSKSPIKTLTELNIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L+A+DRK  GP AP  GLY
Sbjct: 180 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNVWQAEQIKDVLEAKDRKAAGPTAPASGLY 239

Query: 241 FDSVEY 246
           F   EY
Sbjct: 240 FVKTEY 245


>gi|56416825|ref|YP_153899.1| tRNA pseudouridine synthase A [Anaplasma marginale str. St. Maries]
 gi|62901203|sp|Q5PAN6|TRUA_ANAMM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56388057|gb|AAV86644.1| pseudouridylate synthase [Anaplasma marginale str. St. Maries]
          Length = 247

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 113/248 (45%), Positives = 159/248 (64%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY  ++EY+G+ + GWQRQK   G S+Q SIE AI+ ++ + V V  AGRTD+GVHAL 
Sbjct: 1   MRYRAVVEYDGTAFIGWQRQKGVAGRSVQESIEDAIYRLSQQCVTVFAAGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL       ++  ALN YL+ SD +SIL+L    + FHARFSA +R Y+Y+I+ R
Sbjct: 61  QVVHFDLNTSLQDYVIKNALNHYLR-SDMVSILSLEEAAEGFHARFSAKKRHYMYKIVNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-RHDFTTFRSIHCQASSPIRTIDHFDVN 178
            AP  L++ R W +PK L+  +M+ AA H+VG + DF +FR+  CQ+ S +RT+D  D  
Sbjct: 120 DAPPCLDRLRMWHVPKQLNVSDMQEAASHMVGEKKDFASFRAKECQSKSSVRTVDRIDCV 179

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             GN I + V A+SFLH Q+R  VG+L   G G +  + + + L+ ++R   G  APP G
Sbjct: 180 REGNNIFVHVSAKSFLHKQVRIIVGTLVQCGHGAFPPSYVLEILERKNRAAAGITAPPHG 239

Query: 239 LYFDSVEY 246
           LY   VEY
Sbjct: 240 LYLVLVEY 247


>gi|225630801|ref|YP_002727592.1| tRNA pseudouridine synthase A [Wolbachia sp. wRi]
 gi|254764876|sp|C0R4F9|TRUA_WOLWR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|225592782|gb|ACN95801.1| tRNA pseudouridine synthase A [Wolbachia sp. wRi]
          Length = 245

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 114/246 (46%), Positives = 154/246 (62%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EYNGS + GWQ+Q++  +SIQ  IE AIF  +GE + ++  GRTD+GVHAL Q
Sbjct: 1   MRYKITVEYNGSSFSGWQKQQHSANSIQEKIENAIFNFSGEKIALYCGGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+ +E     +  A+N +LK S  I +LN  +VD  FHARFSA +R Y YRI+ R 
Sbjct: 61  VAHFDMEKECELYRIRNAINYHLK-SIPIVVLNAEVVDDAFHARFSAKKRYYEYRIVNRY 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP ALE G  W +   LD   MR AA+HL+G+HD ++FRS  C A++PIRTID  D+   
Sbjct: 120 APAALETGYVWQVFSPLDVNIMREAAKHLLGKHDLSSFRSKDCHAANPIRTIDDIDIVQN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I I++ A SFLH Q+R   G+L   G  +    ++   L    R   G  APP GLY
Sbjct: 180 GNHIHIKISAISFLHNQVRIIAGTLVEFGKNRTNPQEMLHILSQCKRSAAGVTAPPFGLY 239

Query: 241 FDSVEY 246
              ++Y
Sbjct: 240 LVKIDY 245


>gi|222475190|ref|YP_002563606.1| tRNA pseudouridylate synthase A (truA) [Anaplasma marginale str.
           Florida]
 gi|254995027|ref|ZP_05277217.1| tRNA pseudouridine synthase A [Anaplasma marginale str.
           Mississippi]
 gi|255003171|ref|ZP_05278135.1| tRNA pseudouridine synthase A [Anaplasma marginale str. Puerto
           Rico]
 gi|255004302|ref|ZP_05279103.1| tRNA pseudouridine synthase A [Anaplasma marginale str. Virginia]
 gi|254789601|sp|B9KIN8|TRUA_ANAMF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|222419327|gb|ACM49350.1| tRNA pseudouridylate synthase A (truA) [Anaplasma marginale str.
           Florida]
          Length = 247

 Score =  219 bits (558), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 113/248 (45%), Positives = 159/248 (64%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY  ++EY+G+ + GWQRQK   G S+Q SIE AI+ ++ + V V  AGRTD+GVHAL 
Sbjct: 1   MRYRAVVEYDGTAFIGWQRQKGVAGRSVQESIEDAIYRLSQQHVTVFAAGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL       ++  ALN YL+ SD +SIL+L    + FHARFSA +R Y+Y+I+ R
Sbjct: 61  QVVHFDLNTSLQDYVIKNALNHYLR-SDMVSILSLEEAAEGFHARFSAKKRHYMYKIVNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-RHDFTTFRSIHCQASSPIRTIDHFDVN 178
            AP  L++ R W +PK L+  +M+ AA H+VG + DF +FR+  CQ+ S +RT+D  D  
Sbjct: 120 DAPPCLDRLRMWHVPKQLNVSDMQEAASHMVGEKKDFASFRAKECQSKSSVRTVDRIDCV 179

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             GN I + V A+SFLH Q+R  VG+L   G G +  + + + L+ ++R   G  APP G
Sbjct: 180 REGNNIFVHVSAKSFLHKQVRIIVGTLVQCGHGAFPPSYVLEILERKNRAAAGITAPPHG 239

Query: 239 LYFDSVEY 246
           LY   VEY
Sbjct: 240 LYLVLVEY 247


>gi|269958752|ref|YP_003328539.1| tRNA pseudouridine synthase A [Anaplasma centrale str. Israel]
 gi|269848581|gb|ACZ49225.1| tRNA pseudouridine synthase A [Anaplasma centrale str. Israel]
          Length = 247

 Score =  219 bits (558), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 113/248 (45%), Positives = 158/248 (63%), Gaps = 4/248 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY  ++EY+G+ + GWQRQK   G S+Q SIE AI+ ++ + V V  AGRTD+GVHAL 
Sbjct: 1   MRYRAVVEYDGTAFIGWQRQKGVAGRSVQESIEDAIYRLSQQYVTVFAAGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL       ++  ALN YL+ SD +SIL+L    + FHARFSA +R Y+Y+I+ R
Sbjct: 61  QVVHFDLNTSLQDYVIKNALNHYLR-SDMVSILSLEEAAEGFHARFSAKKRHYMYKIVNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-RHDFTTFRSIHCQASSPIRTIDHFDVN 178
            AP  L++ R W +PK L   +M+ AA H+VG + DF +FR+  CQ+ S +RT+D  D  
Sbjct: 120 DAPPCLDRLRMWHVPKQLSVSDMQEAASHMVGEKKDFASFRAKECQSKSSVRTVDRIDCV 179

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             GN I + V A+SFLH Q+R  VG+L   G G +  + + + L+ ++R   G  APP G
Sbjct: 180 REGNNIFVHVSAKSFLHKQVRIIVGTLVQCGHGAFPPSYVLEILERKNRAAAGITAPPHG 239

Query: 239 LYFDSVEY 246
           LY   VEY
Sbjct: 240 LYLVLVEY 247


>gi|239948364|ref|ZP_04700117.1| tRNA pseudouridine synthase A [Rickettsia endosymbiont of Ixodes
           scapularis]
 gi|239922640|gb|EER22664.1| tRNA pseudouridine synthase A [Rickettsia endosymbiont of Ixodes
           scapularis]
          Length = 245

 Score =  218 bits (555), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 108/246 (43%), Positives = 152/246 (61%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQ+Q    S+Q  +E+AI+ ++GE V++ G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTNLAGWQKQAGVMSVQQILEEAIYKLSGEQVILFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  +  A+N Y      + + N  +    FHARFSA  R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPHKIIAAIN-YFARPYAVGVWNCELAPNNFHARFSATSRHYIYRIINRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FR+  CQ+ SPI+T+   ++   
Sbjct: 120 YPSVIDLNRAWWISSPLDILAMQKAASYLLGKHDFTSFRASSCQSKSPIKTLTELNIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L+A+DRK  GP AP  GLY
Sbjct: 180 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNVWQAEQIKDVLEAKDRKAAGPTAPASGLY 239

Query: 241 FDSVEY 246
           F   EY
Sbjct: 240 FVKAEY 245


>gi|42520874|ref|NP_966789.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           melanogaster]
 gi|51316700|sp|Q73G93|TRUA_WOLPM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|42410614|gb|AAS14723.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           melanogaster]
          Length = 245

 Score =  218 bits (555), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 117/246 (47%), Positives = 157/246 (63%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EYNGS + GWQ+Q++  +SIQ  IE AIF  +GE V ++  GRTD+GVHAL Q
Sbjct: 1   MRYKITVEYNGSNFSGWQKQQHSANSIQEKIENAIFNFSGEKVTLYCGGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+ +E+    +  A+N +LK S  I +LN  +VD  FHARFSA +R Y YRI+ R 
Sbjct: 61  VAHFDMEKEFELYRIRNAINYHLK-SIPIVVLNAEVVDDAFHARFSAKKRYYEYRIVNRY 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP ALE G  W +   LD   MR AA+HL+G+HD ++FRS  CQA++PIRTID  D+   
Sbjct: 120 APAALETGYVWQVFSPLDVNIMREAAKHLLGKHDLSSFRSKDCQAANPIRTIDDIDIIQN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I I++ A SFLH Q+R  VG+L   G  +    ++   L    R   G  APP GLY
Sbjct: 180 GNHIHIKISAISFLHNQVRIIVGTLVEFGKNRTNPQEMLNILNQCKRSAAGVTAPPFGLY 239

Query: 241 FDSVEY 246
              ++Y
Sbjct: 240 LVKIDY 245


>gi|157829158|ref|YP_001495400.1| tRNA pseudouridine synthase A [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165933887|ref|YP_001650676.1| tRNA pseudouridine synthase A [Rickettsia rickettsii str. Iowa]
 gi|166228760|sp|A8GU17|TRUA_RICRS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030139|sp|B0BVL0|TRUA_RICRO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157801639|gb|ABV76892.1| tRNA pseudouridine synthase A [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165908974|gb|ABY73270.1| tRNA pseudouridine synthase A [Rickettsia rickettsii str. Iowa]
          Length = 245

 Score =  218 bits (554), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 108/246 (43%), Positives = 152/246 (61%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQRQ    S+Q  +E+AI+  +GE V++ GAGRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTDLAGWQRQAGVMSVQQILEEAIYKFSGEQVILFGAGRTDAGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  +  A+N +++    + + N  +    FHARFSA  R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPHKIITAINYFVR-PYAVGVWNCELAPNNFHARFSATSRYYIYRIINRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FR+  CQ+ SPI+T+   ++   
Sbjct: 120 YPSVIDLNRAWWISSPLDVPAMQQAAAYLLGKHDFTSFRASSCQSKSPIKTLTELNIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L+A+DRK  GP AP  GLY
Sbjct: 180 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNIWQAEQIKDVLEAKDRKAAGPTAPASGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FVKAAY 245


>gi|51474025|ref|YP_067782.1| tRNA pseudouridine synthase A [Rickettsia typhi str. Wilmington]
 gi|62901283|sp|Q68VQ6|TRUA_RICTY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|51460337|gb|AAU04300.1| Pseudouridine synthase [Rickettsia typhi str. Wilmington]
          Length = 245

 Score =  217 bits (553), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 108/246 (43%), Positives = 152/246 (61%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+ + GWQRQ    S+Q  +E+AI+  +GE V + G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTHFSGWQRQAGVLSVQQILEEAIYKFSGEQVTLFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +AHFDL +   P  + KA+N +++    + + N  +V   FHARFSA  R Y+YRI+ R 
Sbjct: 61  IAHFDLSKYLEPYKIIKAINYFVR-PYAVGVWNCELVSNNFHARFSATSRHYIYRIVNRT 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  R W I   LD   M+ AA +L+G+HDFT+FRS  CQ+ SPI+T+   ++   
Sbjct: 120 YPSVIDLNRVWWISAPLDVLAMQQAATYLLGKHDFTSFRSSSCQSKSPIKTLTEINIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W    ++  L A+DRK  GP AP  GLY
Sbjct: 180 YEEIKLYLSAPSFLHYMVRNIVGSLVLVGKNIWQVEQIKNVLDAKDRKVAGPTAPAFGLY 239

Query: 241 FDSVEY 246
           F   EY
Sbjct: 240 FIKAEY 245


>gi|88607493|ref|YP_505097.1| tRNA pseudouridine synthase A [Anaplasma phagocytophilum HZ]
 gi|123722826|sp|Q2GKK4|TRUA_ANAPZ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|88598556|gb|ABD44026.1| tRNA pseudouridine synthase A [Anaplasma phagocytophilum HZ]
          Length = 246

 Score =  217 bits (552), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 109/247 (44%), Positives = 156/247 (63%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY  ++EY G+ + GWQRQ    G S+Q SIE++I     + V+V+ AGRTD+GVHA  
Sbjct: 1   MRYKAVVEYEGTSFIGWQRQHGVVGKSVQESIERSIKEFCQQSVIVYAAGRTDAGVHATG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFDL       ++  ALN YL+ ++ +SIL L  VD++FHARFSA +R Y Y+I  R
Sbjct: 61  QVVHFDLKVSREDYVIKNALNHYLR-NEKVSILQLERVDEEFHARFSAKKRHYTYKISNR 119

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +APL ++  R W +PK L+ ENMR AA ++VG+HDF +FR+  CQ+ S I+T+D  D+ +
Sbjct: 120 EAPLCIDLMRMWHVPKRLNVENMREAASYIVGKHDFASFRAKDCQSKSSIKTVDSIDIIA 179

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I I + A+SFLH Q+R  VG+    G G +    + + L+ +DR   G  AP  GL
Sbjct: 180 AEEEININISAQSFLHKQVRITVGTFVECGMGLYPPAHVLEILEKKDRAAAGITAPAHGL 239

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 240 YLTRVDY 246


>gi|332185222|ref|ZP_08386971.1| tRNA pseudouridine synthase A [Sphingomonas sp. S17]
 gi|332014946|gb|EGI57002.1| tRNA pseudouridine synthase A [Sphingomonas sp. S17]
          Length = 223

 Score =  217 bits (552), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 113/220 (51%), Positives = 146/220 (66%), Gaps = 1/220 (0%)

Query: 27  IQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKIS 86
           +Q ++E AI  VTGE   VH AGRTD+GVH L   AH D+ +   P  L +A+NA ++ +
Sbjct: 1   MQQALEDAIHAVTGERTAVHAAGRTDAGVHGLAMRAHVDIAKVIAPFRLMEAINARIRPA 60

Query: 87  DTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAA 146
             +++L+   V   +HARFS IRRSY YRI+ R+APL  E G AW +P++LD   M  AA
Sbjct: 61  -PVAVLDCVEVASDWHARFSCIRRSYEYRIVNRRAPLTHELGLAWQVPQALDEAAMAEAA 119

Query: 147 QHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLK 206
             LVGRHDFTTFRS+HCQA SP+RT+D   V   G  + IR  ARSFLH Q+RS VG L 
Sbjct: 120 ARLVGRHDFTTFRSVHCQADSPVRTLDLLSVERDGARLFIRAAARSFLHHQVRSMVGCLA 179

Query: 207 LVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           LVG G+WT  D+E AL A+DR + G  AP +GL+F   +Y
Sbjct: 180 LVGMGRWTPDDVEAALVARDRAQLGLNAPSDGLFFVRADY 219


>gi|238651103|ref|YP_002916961.1| tRNA pseudouridine synthase A [Rickettsia peacockii str. Rustic]
 gi|259550439|sp|C4K2W2|TRUA_RICPU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238625201|gb|ACR47907.1| tRNA pseudouridine synthase A [Rickettsia peacockii str. Rustic]
          Length = 245

 Score =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 108/246 (43%), Positives = 150/246 (60%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQRQ    S+Q  +E+AI+  +GE V++ G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTDLAGWQRQAGVMSVQQILEEAIYKFSGEQVILFGSGRTDAGVHAVGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  +  A+N Y      + + N  +    FHARFSA  R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPHKIITAIN-YFARPYAVGVWNCELAPNNFHARFSATSRYYIYRIINRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FR+  CQ+ SPI+T+   ++   
Sbjct: 120 CPSVIDLNRAWWISSPLDVPAMQQAAAYLLGKHDFTSFRASSCQSKSPIKTLTELNIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L+A+DRK  GP AP  GLY
Sbjct: 180 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNIWQAEQIKDVLEAKDRKAAGPTAPASGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FVKAAY 245


>gi|294678738|ref|YP_003579353.1| tRNA pseudouridine synthase A [Rhodobacter capsulatus SB 1003]
 gi|294477558|gb|ADE86946.1| tRNA pseudouridine synthase A [Rhodobacter capsulatus SB 1003]
          Length = 255

 Score =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 111/251 (44%), Positives = 155/251 (61%), Gaps = 5/251 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+   IEY+G  + GWQRQ    S+QG++E A+  +      +  AGRTD+GVHA  Q
Sbjct: 1   MPRFAFRIEYDGGPFAGWQRQAVLPSVQGAVEAALARLEPGEHTIAAAGRTDAGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL ++W P  L +ALN +L+  D ++I+  + V   FHARFSA  R YL+R+++R+
Sbjct: 61  VAHADLAKDWDPFRLSEALNHHLR-PDPVAIVACARVGDDFHARFSARERRYLFRLVSRR 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP+  ++G+ W +   LD   MR  A  L+G HDFTTFR+  CQA SP++T+D   +   
Sbjct: 120 APVVHDRGKVWQVQNPLDVAAMREGAAQLIGLHDFTTFRAAMCQAKSPVKTLDEITIEEI 179

Query: 181 ----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
               G      + ARSFLH Q+RS VG+L+ VG G W   D+ +AL A+DR  CGP+ PP
Sbjct: 180 ALPSGREYRFHLRARSFLHNQVRSIVGTLERVGAGAWAPEDVGRALAARDRAACGPVCPP 239

Query: 237 EGLYFDSVEYS 247
           +GLY   V Y 
Sbjct: 240 QGLYLCGVGYP 250


>gi|114798579|ref|YP_759245.1| tRNA pseudouridine synthase A [Hyphomonas neptunium ATCC 15444]
 gi|123028359|sp|Q0C4U8|TRUA_HYPNA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|114738753|gb|ABI76878.1| tRNA pseudouridine synthase A [Hyphomonas neptunium ATCC 15444]
          Length = 247

 Score =  216 bits (549), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 114/246 (46%), Positives = 151/246 (61%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEYNG  Y GW R     ++QG++E A   + G  V V GAGRTD+GVHA  Q
Sbjct: 1   MPRYRLLIEYNGGPYQGWMRLPGLQTVQGALEAAAAQLDGGPVEVTGAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAH DL R   P  +  A+N +L+    I++L    V++ FHARFSAI R Y Y +I R+
Sbjct: 61  VAHMDL-RVDRPNKVADAMNYHLR-PHPIAVLKADRVEEDFHARFSAIARHYRYIVINRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A L  ++G AW +P  LD + M  AAQ  VG HDFTTFR   CQA SP++T+   DV  +
Sbjct: 119 AHLTHDQGLAWRVPSRLDADKMHEAAQSFVGTHDFTTFRDSECQALSPVKTLTRLDVARY 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + IE    A SF+H Q+RS VGSL  VG G+       + L+A DR  CGP+AP +GL+
Sbjct: 179 NDRIEFTCSAPSFIHRQVRSLVGSLVEVGRGRHPVKWAREILEAADRTRCGPVAPSDGLF 238

Query: 241 FDSVEY 246
            + V+Y
Sbjct: 239 LERVDY 244


>gi|190571328|ref|YP_001975686.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|213018724|ref|ZP_03334532.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|238057739|sp|B3CMC1|TRUA_WOLPP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|190357600|emb|CAQ55041.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|212995675|gb|EEB56315.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 245

 Score =  216 bits (549), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 113/246 (45%), Positives = 156/246 (63%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + IEYNGS + GWQ+Q++  +SIQ +IE AIF  +GE V +H  GRTD+GVHAL Q
Sbjct: 1   MRYKITIEYNGSSFSGWQKQQHSANSIQETIENAIFNFSGERVSLHCGGRTDTGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHF++ R++    +   +N +LK +  I +L+   VD  FHARFSA +R Y YRII R 
Sbjct: 61  VAHFNMERQFELYRIRNGINYHLK-AIPIVVLSAEAVDDAFHARFSAKKRYYEYRIINRY 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP ALE G  W +   LD   MR AA+HL+G+H+ ++FRS  CQA++P+RTID  D+   
Sbjct: 120 APAALEIGYVWQVFNPLDVNIMREAARHLLGKHNLSSFRSKDCQATNPVRTIDDIDIVQN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I++ A SFLH Q+R  VG+L   G  +    ++   L    R   G  APP GLY
Sbjct: 180 GSHIYIKISAISFLHNQVRIIVGTLVEFGKNRTNPQEMLNILSQCKRNAAGITAPPHGLY 239

Query: 241 FDSVEY 246
              ++Y
Sbjct: 240 LVKIDY 245


>gi|15893251|ref|NP_360965.1| tRNA pseudouridine synthase A [Rickettsia conorii str. Malish 7]
 gi|24212567|sp|Q92FZ9|TRUA_RICCN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|15620470|gb|AAL03866.1| pseudouridylate synthase I [Rickettsia conorii str. Malish 7]
          Length = 245

 Score =  216 bits (549), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 108/246 (43%), Positives = 150/246 (60%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQRQ    S+Q  +E+AI+  +GE V++ G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTDLAGWQRQAGVMSVQQILEEAIYKFSGEQVILFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  +  A+N Y      + + N  +    FHARFSA  R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPHKIITAIN-YFARPYAVGVWNCELAPNNFHARFSATSRYYIYRIINRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FR+  CQ+ SPI+T+   ++   
Sbjct: 120 YPSVIDLNRAWWISAPLDVPAMQQAAVYLLGKHDFTSFRASSCQSKSPIKTLTELNIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L+A+DRK  GP AP  GLY
Sbjct: 180 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNIWQAEQIKDVLEAKDRKAAGPTAPASGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FVKTAY 245


>gi|296115065|ref|ZP_06833707.1| tRNA pseudouridine synthase A [Gluconacetobacter hansenii ATCC
           23769]
 gi|295978402|gb|EFG85138.1| tRNA pseudouridine synthase A [Gluconacetobacter hansenii ATCC
           23769]
          Length = 283

 Score =  215 bits (548), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 119/249 (47%), Positives = 159/249 (63%), Gaps = 7/249 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVH-GAGRTDSGVHALRQ 60
           R+ + IEY+G  + GWQRQ +G +S+QG +E A   +TG   V+   AGRTDSGVHA  Q
Sbjct: 30  RWAVRIEYDGRDFVGWQRQASGLTSVQGVLEAAATRLTGGRPVISITAGRTDSGVHATGQ 89

Query: 61  VAHFDLVREWVPV---ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           VAH D   + +P+    +  ALN ++K    ++IL    V   + ARFSAI RSY YRII
Sbjct: 90  VAHLDFPDD-IPLSSTAVRDALNYHMK-PHRVAILIARPVLPNWSARFSAILRSYRYRII 147

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R A   L++GR W + + LD + MR AAQ L+GRHDFTTFR+  CQA SP+RT+D  D+
Sbjct: 148 NRSARPTLDEGRVWHVRQPLDVDLMRQAAQFLIGRHDFTTFRASACQAKSPVRTLDRLDI 207

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G  I I   AR+FLH Q+R+  G+LK+VG+G W+   + +AL A DR+  GP AP E
Sbjct: 208 HREGEEIVIVTEARAFLHHQVRNMTGTLKMVGEGSWSVERVGQALAACDRRAGGPTAPAE 267

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 268 GLYLTGVAY 276


>gi|91204875|ref|YP_537230.1| tRNA pseudouridine synthase A [Rickettsia bellii RML369-C]
 gi|157826493|ref|YP_001495557.1| tRNA pseudouridine synthase A [Rickettsia bellii OSU 85-389]
 gi|123266250|sp|Q1RKH3|TRUA_RICBR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228758|sp|A8GUM4|TRUA_RICB8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91068419|gb|ABE04141.1| tRNA pseudouridine synthase A [Rickettsia bellii RML369-C]
 gi|157801797|gb|ABV78520.1| tRNA pseudouridine synthase A [Rickettsia bellii OSU 85-389]
          Length = 245

 Score =  213 bits (543), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 104/246 (42%), Positives = 152/246 (61%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + +EY G+   GWQRQ    S+Q  +E+AI+  +GE V + G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKISVEYLGTNLAGWQRQSGVMSVQQILEEAIYKFSGEQVTLFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +AHFDL + + P  + +A+N Y      + + N  +VD  FHARFSAI R Y+YRI+ R 
Sbjct: 61  IAHFDLSKYFEPYKIIRAIN-YFTRPYIVGVCNCELVDNNFHARFSAIARHYVYRILNRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  R W I   LD   M+ ++ +L+G+H+FT+FR+  CQ+ SPI+T+   D+   
Sbjct: 120 YPSVIDFDRVWWISVPLDVSAMQKSSLYLLGKHNFTSFRASSCQSKSPIKTLTKLDIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++   A SFLH  +R+ VGSL LVG   W +  +++ L+  DRK  GP AP  GLY
Sbjct: 180 NEEIKLYFSAPSFLHHMVRNIVGSLVLVGKNIWQAEQMQQVLEVADRKAAGPTAPACGLY 239

Query: 241 FDSVEY 246
           F   +Y
Sbjct: 240 FIKADY 245


>gi|258541768|ref|YP_003187201.1| tRNA pseudouridine synthase A [Acetobacter pasteurianus IFO
           3283-01]
 gi|256632846|dbj|BAH98821.1| tRNA pseudouridine synthase A TruA [Acetobacter pasteurianus IFO
           3283-01]
 gi|256635903|dbj|BAI01872.1| tRNA pseudouridine synthase A TruA [Acetobacter pasteurianus IFO
           3283-03]
 gi|256638958|dbj|BAI04920.1| tRNA pseudouridine synthase A TruA [Acetobacter pasteurianus IFO
           3283-07]
 gi|256642012|dbj|BAI07967.1| tRNA pseudouridine synthase A TruA [Acetobacter pasteurianus IFO
           3283-22]
 gi|256645067|dbj|BAI11015.1| tRNA pseudouridine synthase A TruA [Acetobacter pasteurianus IFO
           3283-26]
 gi|256648122|dbj|BAI14063.1| tRNA pseudouridine synthase A TruA [Acetobacter pasteurianus IFO
           3283-32]
 gi|256651175|dbj|BAI17109.1| tRNA pseudouridine synthase A TruA [Acetobacter pasteurianus IFO
           3283-01-42C]
 gi|256654166|dbj|BAI20093.1| tRNA pseudouridine synthase A TruA [Acetobacter pasteurianus IFO
           3283-12]
          Length = 262

 Score =  213 bits (541), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 115/255 (45%), Positives = 159/255 (62%), Gaps = 20/255 (7%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + +EY+G+G  GWQRQK+G S+Q  +E+A   L     V    AGRTDSGVHAL QV
Sbjct: 11  RWAVKLEYDGTGLVGWQRQKSGLSVQSLLEEAAARLANNRPVSSITAGRTDSGVHALAQV 70

Query: 62  AHFDL----------VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRS 111
           AH D           VRE         L+ +LK  + + +L+ + VD  + ARFSAI RS
Sbjct: 71  AHLDFPADVRFSRHSVRE--------GLSYHLKPHNVV-VLDAAQVDTDWSARFSAIWRS 121

Query: 112 YLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           Y YRI+ R++   L  G+ W +  +LD E M+ AA  LVG HDFT+FR++ CQA SP+RT
Sbjct: 122 YQYRILNRRSRPTLLAGQVWHVKSTLDVEKMQEAANILVGSHDFTSFRAVACQAHSPMRT 181

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           +D  +++  G+ + +   ARSFLH Q+R+ VG+LKLVG G W    + +AL+A++R   G
Sbjct: 182 LDQLEISRHGDEVIVFAKARSFLHHQVRNMVGTLKLVGIGAWQPERVAEALEARNRCAAG 241

Query: 232 PLAPPEGLYFDSVEY 246
           P APPEGLY + V Y
Sbjct: 242 PTAPPEGLYLNGVGY 256


>gi|157826343|ref|YP_001494063.1| tRNA pseudouridine synthase A [Rickettsia akari str. Hartford]
 gi|166228757|sp|A8GQ80|TRUA_RICAH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157800301|gb|ABV75555.1| tRNA pseudouridine synthase A [Rickettsia akari str. Hartford]
          Length = 245

 Score =  212 bits (540), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 109/246 (44%), Positives = 152/246 (61%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQRQ    S+Q  +E+AI+  +GE V++ G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTNLAGWQRQAGVMSVQQILEEAIYKFSGEQVILFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  +  A+N Y      + + + +IV   FHARFSA  R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPHKIITAIN-YFARPYAVVVWHCAIVLNDFHARFSATSRHYIYRIINRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FR+  CQ+ SPI+T+   ++   
Sbjct: 120 YPSVIDLNRAWWISSPLDVLAMQKAAAYLLGKHDFTSFRASSCQSKSPIKTLTELNIVKG 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L+A+DRK  G  AP  GLY
Sbjct: 180 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNIWQAEHIKDVLEAKDRKAAGLTAPAYGLY 239

Query: 241 FDSVEY 246
           F   EY
Sbjct: 240 FVKTEY 245


>gi|34581081|ref|ZP_00142561.1| pseudouridylate synthase I [Rickettsia sibirica 246]
 gi|28262466|gb|EAA25970.1| pseudouridylate synthase I [Rickettsia sibirica 246]
          Length = 245

 Score =  212 bits (540), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 107/246 (43%), Positives = 149/246 (60%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQRQ    S+Q  +E+AI+  +GE V++ G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTDLAGWQRQAGVMSVQQILEEAIYKFSGEQVILFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  +  A+N Y      + + N  +    FHARFSA  R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPHKIITAIN-YFARPYAVGVWNCELAPNNFHARFSATSRYYIYRIINRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FR+  CQ+ S I+T+   ++   
Sbjct: 120 YPSVIDLNRAWWISSPLDVPAMQQAAVYLLGKHDFTSFRASSCQSKSSIKTLTELNIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L+A+DRK  GP AP  GLY
Sbjct: 180 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNIWQAEQIKDVLEAKDRKAAGPTAPASGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FVKTAY 245


>gi|229587225|ref|YP_002845726.1| tRNA pseudouridine synthase A [Rickettsia africae ESF-5]
 gi|259550437|sp|C3PLZ3|TRUA_RICAE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|228022275|gb|ACP53983.1| tRNA pseudouridine synthase A [Rickettsia africae ESF-5]
          Length = 245

 Score =  211 bits (536), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 107/246 (43%), Positives = 148/246 (60%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQRQ    S+Q  +E+AI+  +GE V++ G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTDLAGWQRQAGVMSVQQILEEAIYKFSGEQVILFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  +  A+N Y      + + N  +    FHARFSA  R Y+YRII R 
Sbjct: 61  VAHFDLSKYLEPHKIITAIN-YFARPYAVGVWNCELAPNNFHARFSATSRYYIYRIINRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ AA +L+G+HDFT+FR+  CQ+ S I+T+   ++   
Sbjct: 120 YPSVIDLNRAWWISSPLDVPAMQQAAVYLLGKHDFTSFRASSCQSKSSIKTLTELNIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W    ++  L+A+DRK  GP AP  GLY
Sbjct: 180 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNIWQVEQIKDVLEAKDRKAAGPTAPASGLY 239

Query: 241 FDSVEY 246
           F    Y
Sbjct: 240 FVKTAY 245


>gi|88608581|ref|YP_505923.1| tRNA pseudouridine synthase A [Neorickettsia sennetsu str.
           Miyayama]
 gi|123763741|sp|Q2GF33|TRUA_NEOSM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|88600750|gb|ABD46218.1| tRNA pseudouridine synthase A [Neorickettsia sennetsu str.
           Miyayama]
          Length = 243

 Score =  210 bits (534), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 110/247 (44%), Positives = 156/247 (63%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY  I+EY G+G+ GWQ+Q +  S+Q  +E  +  +  E + V+ AGRTD+GVHAL QV
Sbjct: 1   MRYKAIVEYVGTGFSGWQKQMSAPSVQEELESVLSFLLKEKIAVNVAGRTDAGVHALGQV 60

Query: 62  AHFDLVREWV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HFD  RE    P  +  A+N +LK    I +L + IVD+ F ARFSAIRR Y Y+I  R
Sbjct: 61  FHFD-ARESTLQPFQIVNAVNYHLK-EKLIVLLKIEIVDETFDARFSAIRRHYQYKITNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + PLA+ K R+W +P++L+ + +R  AQ+LVG+HDF +FRS  C AS+ IRT+D  +V  
Sbjct: 119 KTPLAVFKNRSWHVPQTLNLDLIREQAQYLVGKHDFQSFRSSKCGASNAIRTLDRLEVEK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  +     A+SFLH Q+R  VG+L  +  GK  S  + + L  ++R+  GP APP GL
Sbjct: 179 NGEEMIFHASAKSFLHHQVRIMVGTLVAIASGKLMS--VTEILSKKNRRYAGPTAPPCGL 236

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 237 YLLKVDY 243


>gi|114327354|ref|YP_744511.1| tRNA pseudouridine synthase A [Granulibacter bethesdensis CGDNIH1]
 gi|114315528|gb|ABI61588.1| tRNA pseudouridine synthase A [Granulibacter bethesdensis CGDNIH1]
          Length = 270

 Score =  208 bits (529), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 120/255 (47%), Positives = 160/255 (62%), Gaps = 11/255 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSS---------IQGSIEKAIF-LVTGEIVVVHGAGRTD 52
           RY + IEY+G+ + GWQRQ    S         +Q  +E+A   L  GE V    AGRTD
Sbjct: 12  RYALRIEYDGTPFIGWQRQGTDDSATAQGRAVSVQWVLEQAAARLARGEAVSSIVAGRTD 71

Query: 53  SGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSY 112
           +GVHA  QVA  DL   + P  + +ALN ++K    ++IL  +     ++ARFSAI RSY
Sbjct: 72  AGVHAQAQVAQIDLPTAFHPERVREALNFHMKPY-PVAILEAAYAPDGWNARFSAIGRSY 130

Query: 113 LYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTI 172
            Y I+ R+A  AL +GR W + + LD + M  AA+HL+GRHDFT+FR+  CQA SP+RT+
Sbjct: 131 RYLILNRRARPALMEGRVWHVAQPLDADTMDGAAKHLLGRHDFTSFRAAACQAKSPLRTL 190

Query: 173 DHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP 232
           D  DV   G+LI I   ARSFLH Q+R+ VG+LKLVGDG+WT+  +  AL A+DR + GP
Sbjct: 191 DRLDVRRDGDLITIIAEARSFLHHQVRNMVGTLKLVGDGRWTAEHVAAALAARDRAKAGP 250

Query: 233 LAPPEGLYFDSVEYS 247
            APP+GL    V Y 
Sbjct: 251 TAPPDGLALTGVIYE 265


>gi|157804248|ref|YP_001492797.1| tRNA pseudouridine synthase A [Rickettsia canadensis str. McKiel]
 gi|166228759|sp|A8F079|TRUA_RICCK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157785511|gb|ABV74012.1| tRNA pseudouridine synthase A [Rickettsia canadensis str. McKiel]
          Length = 245

 Score =  208 bits (529), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 105/246 (42%), Positives = 150/246 (60%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQRQ    S+Q  +E+AI+  +GE VV+ G+GRTD+GVHA+ Q
Sbjct: 1   MYRYKITIEYLGTDLAGWQRQAGIMSVQQILEEAIYKFSGEQVVLFGSGRTDAGVHAIGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +      +  A+N + +    I + N  +    FHARFSA+ R Y+YRI+ R 
Sbjct: 61  VAHFDLSKNLETHKIITAINYFARPYSVI-VWNCEMAPNNFHARFSAVSRHYIYRILNRP 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               + + R W I   LD   M+ AA +L+G+HDFT+FR+  CQ+ SPI+T+   ++   
Sbjct: 120 YSSVINRDRVWWISSPLDVLAMQKAATYLLGKHDFTSFRASSCQSKSPIKTLTELNIIKE 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  +++ L+ +DRK  GP AP  GLY
Sbjct: 180 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNVWQAEYIKELLEVKDRKAAGPTAPASGLY 239

Query: 241 FDSVEY 246
           F   EY
Sbjct: 240 FVRTEY 245


>gi|329114449|ref|ZP_08243211.1| tRNA pseudouridine synthase A [Acetobacter pomorum DM001]
 gi|326696525|gb|EGE48204.1| tRNA pseudouridine synthase A [Acetobacter pomorum DM001]
          Length = 262

 Score =  206 bits (525), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 113/247 (45%), Positives = 157/247 (63%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH-GAGRTDSGVHALRQV 61
           R+ + +EY+G+G  GWQRQK+G S+Q  +E A   + G   V    AGRTDSGVHAL QV
Sbjct: 11  RWAVKLEYDGTGLVGWQRQKSGLSVQSLLEAAAARLAGNRPVSSITAGRTDSGVHALAQV 70

Query: 62  AHFDLVRE--WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AH D   +  +    + + L+ +LK  + + +L+   VD  + ARFSA  RSY YRI+ R
Sbjct: 71  AHLDFPADVRFSRHSVREGLSYHLKPHNVV-VLDAVQVDTDWSARFSATWRSYQYRILNR 129

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++   L  G  W +  +LD E M+ AA  LVG HDFT+FR++ CQA SP+RT+D  DV+ 
Sbjct: 130 RSRPTLLAGNVWHVKSTLDVEKMQEAANILVGPHDFTSFRAVACQAHSPMRTLDQLDVSR 189

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + +   ARSFLH Q+R+ VG+LKLVG G W    + +AL+A++R   GP APPEGL
Sbjct: 190 HGDEVLVFAKARSFLHHQVRNMVGTLKLVGIGAWQPERVAEALEARNRCAAGPTAPPEGL 249

Query: 240 YFDSVEY 246
           Y + V Y
Sbjct: 250 YLNGVGY 256


>gi|162147913|ref|YP_001602374.1| tRNA pseudouridine synthase A [Gluconacetobacter diazotrophicus PAl
           5]
 gi|209542530|ref|YP_002274759.1| tRNA pseudouridine synthase A [Gluconacetobacter diazotrophicus PAl
           5]
 gi|161786490|emb|CAP56072.1| putative tRNA pseudouridine synthase A [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209530207|gb|ACI50144.1| tRNA pseudouridine synthase A [Gluconacetobacter diazotrophicus PAl
           5]
          Length = 258

 Score =  204 bits (520), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 115/247 (46%), Positives = 154/247 (62%), Gaps = 4/247 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + IEY+G  + GWQRQ  G S+Q  +E+A   L +G +V    AGRTD+GVHA  Q 
Sbjct: 8   RWAVRIEYDGRPFVGWQRQITGLSVQQVLEEAASRLASGRVVPSITAGRTDAGVHATGQA 67

Query: 62  AHFDLVRE--WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           AH D   +       +  ALN ++K    +++L    VD ++ ARFSAIRRSY YRI+ R
Sbjct: 68  AHLDFPGDVRLNDSTVRDALNFHMKPY-PVAVLRACPVDTEWSARFSAIRRSYRYRILNR 126

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           ++   L+ GR WL+ ++LD   M  AA+ L+GRHDFT+FR+  CQA SP+RT+D   V  
Sbjct: 127 RSRPTLDDGRVWLVKRTLDEAAMARAARLLLGRHDFTSFRASACQARSPLRTLDRLGVVR 186

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I I   ARSFLH Q+R+ VG+LKLVG+G W    +  AL A DR+  GP APP+GL
Sbjct: 187 QGEEIVIEAEARSFLHHQVRNMVGTLKLVGEGLWAPDRVAAALAACDRRAAGPTAPPDGL 246

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 247 YLTGVGY 253


>gi|148259428|ref|YP_001233555.1| tRNA pseudouridine synthase A [Acidiphilium cryptum JF-5]
 gi|326402654|ref|YP_004282735.1| tRNA pseudouridine synthase A [Acidiphilium multivorum AIU301]
 gi|166228673|sp|A5FVK4|TRUA_ACICJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|146401109|gb|ABQ29636.1| tRNA pseudouridine synthase A [Acidiphilium cryptum JF-5]
 gi|325049515|dbj|BAJ79853.1| tRNA pseudouridine synthase A [Acidiphilium multivorum AIU301]
          Length = 255

 Score =  204 bits (518), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 110/247 (44%), Positives = 147/247 (59%), Gaps = 1/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M R+ + +EY+G G+ GWQRQ+NG S+Q  +E A   L  G++     AGRTD+GVHA  
Sbjct: 1   MRRWALRLEYDGRGFVGWQRQENGLSVQEVLETAASRLCGGDVPDSVVAGRTDAGVHAAG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA  +L        + +ALN ++K      I         +  RFSAI R+Y Y I+ R
Sbjct: 61  QVAALELPDRLDARAVREALNFHMKPHAVAVIEAAPAPSAAWSPRFSAIGRAYRYLILNR 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            A  AL  G  W +   LD   M  AAQ L+GRHDFT+FR+  CQA+SP+RT+D  DV  
Sbjct: 121 SARPALRDGFVWHVKAPLDAPAMHEAAQSLLGRHDFTSFRASSCQANSPLRTLDRLDVRR 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I   ARSFLH Q+R+ VG+LKLVG+G+W    + +AL A+DR   GP APP+GL
Sbjct: 181 DGETVVIEAEARSFLHHQVRNMVGTLKLVGEGRWRVGRVAEALAARDRSAAGPTAPPDGL 240

Query: 240 YFDSVEY 246
              +V Y
Sbjct: 241 VLVAVRY 247


>gi|254796418|ref|YP_003081254.1| tRNA pseudouridine synthase A [Neorickettsia risticii str.
           Illinois]
 gi|254589655|gb|ACT69017.1| tRNA pseudouridine synthase A [Neorickettsia risticii str.
           Illinois]
          Length = 243

 Score =  203 bits (517), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 112/247 (45%), Positives = 149/247 (60%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY   +EY G+G+ GWQ+Q +  S+Q  +E  +  +  E + V+ AGRTD+GVHAL QV
Sbjct: 1   MRYKATVEYVGTGFSGWQKQMSAPSVQEELESVLSFLLKEKIAVNVAGRTDAGVHALGQV 60

Query: 62  AHFDLVREWV--PVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HFD  RE    P  +  A+N +LK    I +L + IVD+ F ARFSAIRR Y YRII R
Sbjct: 61  FHFD-ARESTLQPFQIVNAVNYHLK-EKLIVLLKIEIVDETFDARFSAIRRHYQYRIINR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           + P A+ + R W +P  L+ + MR  AQHLVGRHDF +FRS  C AS+ IRT+D  +V  
Sbjct: 119 KMPPAVFRNRCWHVPWKLNLDFMREQAQHLVGRHDFQSFRSSKCGASNAIRTLDRLEVEK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I     A+SFLH Q+R  VG+L  +  GK  S    + L  ++R   GP AP  GL
Sbjct: 179 NGEEIIFHASAKSFLHHQVRIMVGTLVAIASGKLVSAT--EILSKRNRCYAGPTAPSCGL 236

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 237 YLLKVDY 243


>gi|157965031|ref|YP_001499855.1| tRNA pseudouridine synthase A [Rickettsia massiliae MTU5]
 gi|157844807|gb|ABV85308.1| tRNA pseudouridine synthase A [Rickettsia massiliae MTU5]
          Length = 246

 Score =  197 bits (500), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 106/246 (43%), Positives = 149/246 (60%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY + IEY G+   GWQ+Q    S+Q  +E+AI+  +GE V++ G+GRTD+GVHA+ Q
Sbjct: 2   MYRYKITIEYLGTDLAGWQKQAGVMSVQQILEEAIYKFSGEQVILFGSGRTDAGVHAIGQ 61

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFDL +   P  +  A+N Y      + + N  +    FHARFSA  R Y+YRII R 
Sbjct: 62  VAHFDLSKYLEPHKIITAIN-YFARPYAVGVWNCELAPNNFHARFSATSRYYIYRIINRP 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  ++  RAW I   LD   M+ A  +L+G+HDFT+FR+  CQ+ SPI+T+   ++   
Sbjct: 121 YPSVIDLNRAWWISSPLDVPAMQQATAYLLGKHDFTSFRASSCQSKSPIKTLTELNIIKE 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I++ + A SFLH  +R+ VGSL LVG   W +  ++  L+A+DRK  GP AP  GLY
Sbjct: 181 DEEIKLYLSAPSFLHHMVRNIVGSLVLVGKNIWQAEQIKDVLEAKDRKAAGPTAPAAGLY 240

Query: 241 FDSVEY 246
           F    Y
Sbjct: 241 FVKAAY 246


>gi|262277956|ref|ZP_06055749.1| tRNA pseudouridine synthase A [alpha proteobacterium HIMB114]
 gi|262225059|gb|EEY75518.1| tRNA pseudouridine synthase A [alpha proteobacterium HIMB114]
          Length = 245

 Score =  195 bits (496), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 100/246 (40%), Positives = 152/246 (61%), Gaps = 1/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY  ++EYNG+ + GWQ Q +G+++Q  IEK+   +      + G+GRTDSGVHA  Q
Sbjct: 1   MHRYKAVVEYNGTDFEGWQSQPSGNTVQQIIEKSFLEIQLNKTKIFGSGRTDSGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +     +   LN +LK    IS+L+L   +  F +R  A  R+Y Y+I+ R 
Sbjct: 61  VFHFDYEDKLDCKKILLGLNHFLK-KKNISVLSLDFTNNNFDSRRDAKLRTYTYKILNRI 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           A   + + + W + K+LD + M+ A+Q  +G HDFTTFR+  C+A+SPIR I + ++   
Sbjct: 120 ASPVILENQVWHVIKNLDFKLMQKASQIFLGSHDFTTFRASSCEATSPIREIIYSELKKN 179

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I   V +RSFL  Q+RS VG++K VG+ KW+  DL++AL++++R  C   AP  GLY
Sbjct: 180 NDQIIYIVKSRSFLQHQVRSMVGAIKFVGEKKWSLKDLDEALKSKNRNNCATPAPACGLY 239

Query: 241 FDSVEY 246
            ++VEY
Sbjct: 240 LENVEY 245


>gi|58040265|ref|YP_192229.1| tRNA pseudouridine synthase A [Gluconobacter oxydans 621H]
 gi|62901153|sp|Q5FPX3|TRUA_GLUOX RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|58002679|gb|AAW61573.1| tRNA pseudouridine synthase A [Gluconobacter oxydans 621H]
          Length = 275

 Score =  193 bits (490), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 106/248 (42%), Positives = 149/248 (60%), Gaps = 6/248 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + IEY+G+GY GWQ+Q +G+SIQG IE A   LV    V    AGRTD+GVHA   V
Sbjct: 22  RWALRIEYDGTGYLGWQKQNDGTSIQGLIEAAASKLVRNRPVPSITAGRTDAGVHAAGMV 81

Query: 62  AHFDLVREWVPVI---LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            H D   +  P+    +   +  +LK    + +L  + V  +++ARFSA  RSY Y I+ 
Sbjct: 82  IHLDFPDD-APIDARQIRDGMGYHLK-PHRVVVLETAKVGPEWNARFSATWRSYRYTILN 139

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R A   L + R W I + LD + M+ AA HL+G HDFT+FR++ CQA SPIRT+D  +++
Sbjct: 140 RPARPGLMENRVWHIKRPLDVDLMQQAANHLLGPHDFTSFRAVACQARSPIRTLDVLNIH 199

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G L+ I   ARSFLH Q+R+  G+L ++G  +W    + + L+A+DR   G  APPEG
Sbjct: 200 RDGELVMIDTKARSFLHHQVRNMAGTLMMIGSRQWPVEKIIEILEAKDRCAAGQTAPPEG 259

Query: 239 LYFDSVEY 246
           L    V Y
Sbjct: 260 LCLMDVGY 267


>gi|71083164|ref|YP_265883.1| tRNA pseudouridine synthase A [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|123734383|sp|Q4FNF9|TRUA_PELUB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|71062277|gb|AAZ21280.1| tRNA pseudouridine synthase A [Candidatus Pelagibacter ubique
           HTCC1062]
          Length = 246

 Score =  192 bits (489), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 105/248 (42%), Positives = 149/248 (60%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY G+ + GWQ Q  G SIQ  I+  +     E VV+ G+GRTD+GVHA+ Q
Sbjct: 1   MFRYQVLIEYIGTNFVGWQIQSKGKSIQKEIQVKLSKFLKEKVVLIGSGRTDAGVHAIEQ 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            AHFD  +E   +  L K++N +  I+D  IS+L +     +FHAR SA +R Y Y I  
Sbjct: 61  SAHFDCKKEIQNLDKLLKSINHF--INDKGISVLAIKKRSLKFHARHSAKQRIYKYIIFN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R +  +LEK R W I K LD E M+  ++ L+G  DF+TFR+  C A SPI+T+   ++ 
Sbjct: 119 RLSKPSLEKERGWHIIKKLDIELMKKGSKKLLGTKDFSTFRASSCNAKSPIKTMKSVNIK 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           S    IEI+  ++SFL  Q+RS VGSLK + + KW     E  ++++ R  C P AP EG
Sbjct: 179 SKDGRIEIQFKSQSFLQQQVRSMVGSLKYLAENKWDLKKFEFVIKSKKRILCAPPAPAEG 238

Query: 239 LYFDSVEY 246
           L+ + V Y
Sbjct: 239 LFLEKVIY 246


>gi|189183835|ref|YP_001937620.1| tRNA pseudouridine synthase A [Orientia tsutsugamushi str. Ikeda]
 gi|238692245|sp|B3CSN9|TRUA_ORITI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189180606|dbj|BAG40386.1| pseudouridylate synthase I [Orientia tsutsugamushi str. Ikeda]
          Length = 283

 Score =  192 bits (488), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 112/285 (39%), Positives = 157/285 (55%), Gaps = 41/285 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RY  I+EY+G+ + GWQRQ+NG SIQ  +E  I   T + V +  AGRTD+GVHAL Q
Sbjct: 1   MLRYKAIVEYDGTNFVGWQRQQNGLSIQQLLEDKISTFTKQTVNLIAAGRTDAGVHALGQ 60

Query: 61  VAHFDLVR-----------------------------EWVPVILCKALNAYLKISDT--- 88
           V HFDL+                              + + ++ C+  NAY  +S     
Sbjct: 61  VVHFDLISPNNSKDLACINKETDNKEVSKQNNTTTTIDSLKMLPCR-YNAYKLMSAVNYL 119

Query: 89  -----ISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMR 143
                I + +  I   QFHARFSA  R Y YRII R  P  +E+ R W I   L+  +M 
Sbjct: 120 LKPHRIILTSCEITTLQFHARFSAKARHYKYRIINRAVPSVIEQNRTWWIKTPLNVIDMI 179

Query: 144 IAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVV--ARSFLHTQIRSF 201
            A+QHL+G+HDFT+FRS  CQA SP++T+   +V++  N  EI++   A SFLH  +R+ 
Sbjct: 180 DASQHLIGKHDFTSFRSSACQAKSPLKTLTKIEVDT-TNYPEIQIYFSAPSFLHHMVRNI 238

Query: 202 VGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           VG+L  +G  K +   ++  L A++R   GP AP  GLYF  V+Y
Sbjct: 239 VGTLVYIGLCKISPAAIKTILFAKNRAMAGPTAPSSGLYFVKVDY 283


>gi|148284891|ref|YP_001248981.1| tRNA pseudouridine synthase A [Orientia tsutsugamushi str. Boryong]
 gi|166228742|sp|A5CET3|TRUA_ORITB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|146740330|emb|CAM80738.1| tRNA pseudouridine synthase A [Orientia tsutsugamushi str. Boryong]
          Length = 284

 Score =  192 bits (488), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 113/286 (39%), Positives = 156/286 (54%), Gaps = 42/286 (14%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+RY  I+EY+G+ + GWQRQ+NG SIQ  +E  I   T + V +  AGRTD+GVHAL Q
Sbjct: 1   MLRYKAIVEYDGTNFVGWQRQQNGLSIQQLLEDKISTFTKQTVNLIAAGRTDAGVHALGQ 60

Query: 61  VAHFDLV---------------------------------REWVPV-----ILCKALNAY 82
           V HFDL+                                 ++ +P       L  A+N  
Sbjct: 61  VVHFDLIAPNNSKDLACINKETDNKEVSKQNNTTTTIDSLKKMLPCRYNAYKLMSAVNYL 120

Query: 83  LKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENM 142
           LK    I + +  I   QFHARFSA  R Y YRII R  P  +E+ R W I   L+  +M
Sbjct: 121 LK-PHRIILTSCEITTLQFHARFSAKARHYKYRIINRTVPSVIEQNRTWWIKPPLNVIDM 179

Query: 143 RIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVV--ARSFLHTQIRS 200
             A+QHL+G+HDFT+FRS  CQA SP++T+   +V++  N  EI++   A SFLH  +R+
Sbjct: 180 IDASQHLIGKHDFTSFRSSACQAKSPLKTLTKIEVDT-TNYPEIQIYFSAPSFLHHMVRN 238

Query: 201 FVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            VG+L  +G  K +   ++  L A++R   GP AP  GLYF  V+Y
Sbjct: 239 IVGTLVYIGLCKISPAAIKTILFAKNRAMAGPTAPSSGLYFVKVDY 284


>gi|117925388|ref|YP_866005.1| tRNA pseudouridine synthase A [Magnetococcus sp. MC-1]
 gi|117609144|gb|ABK44599.1| tRNA pseudouridine synthase A [Magnetococcus sp. MC-1]
          Length = 270

 Score =  191 bits (486), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 96/244 (39%), Positives = 145/244 (59%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + +E++GS + GWQ Q+N  S+Q ++E+A+  +  E + VHG+GRTD+GVHA  QVA
Sbjct: 14  RFRITVEFDGSAFSGWQSQQNAPSVQQALEQALAPLHNEPIRVHGSGRTDAGVHATGQVA 73

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD           + LN  ++   +I++L    V + FHAR+ A  R YLYRI TR+ P
Sbjct: 74  HFDAPAHRDAATYLRILN--VRTPHSIAVLACQPVAESFHARYDAYYRQYLYRINTRKIP 131

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            ALE+ R W  P  LD E +  A+  L+G HDF++FR+  CQ+ SP++ +        G+
Sbjct: 132 PALERSRVWHYPYLLDAERLAEASALLLGTHDFSSFRAAGCQSKSPVKFMRLIQWQQRGD 191

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
             ++ + A +FL   +R+ VG+L LVG G W    + + L A+DR + GP AP  GLY  
Sbjct: 192 EWQVSIGANAFLQHMVRNLVGTLVLVGKGDWPVARVAELLAARDRVQAGPTAPAWGLYLT 251

Query: 243 SVEY 246
            + Y
Sbjct: 252 HICY 255


>gi|20808627|ref|NP_623798.1| tRNA pseudouridine synthase A [Thermoanaerobacter tengcongensis
           MB4]
 gi|24212532|sp|Q8R7Y7|TRUA_THETN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|20517260|gb|AAM25402.1| Pseudouridylate synthase (tRNA psi55) [Thermoanaerobacter
           tengcongensis MB4]
          Length = 240

 Score =  191 bits (485), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 101/242 (41%), Positives = 144/242 (59%), Gaps = 2/242 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            +IIEY+G+ Y GWQ QKN  ++Q  +EKAI  VTGE V + G+ RTD+GVHAL QVA+F
Sbjct: 1   MLIIEYDGTNYHGWQYQKNAITVQEVLEKAIEKVTGEKVNLIGSSRTDTGVHALYQVANF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +  P  L  ALNA L   D + ++    VDK FHAR+SA  + Y Y I+ RQ P+ 
Sbjct: 61  KTKTKIPPEKLPYALNAVL--PDDVVVVKAKEVDKSFHARYSARSKRYRYLILNRQFPMP 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   W +P  LD E M+ AA    G HDF+ F++   +  +P++TI    V   G+LI
Sbjct: 119 TMRNYCWHVPYPLDVEAMKKAAFFFRGTHDFSAFKASGNKKVNPVKTIFDLTVEKEGDLI 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I V A  FL+  +R  VG+L  VG GK  + ++   ++++DR + G  APP+GLY   +
Sbjct: 179 KIEVEADGFLYNMVRIIVGTLVYVGLGKIKAGEIPAIIESKDRTKAGITAPPQGLYLVRI 238

Query: 245 EY 246
            Y
Sbjct: 239 VY 240


>gi|91762406|ref|ZP_01264371.1| tRNA pseudouridine synthase A [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91718208|gb|EAS84858.1| tRNA pseudouridine synthase A [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 246

 Score =  190 bits (482), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 105/248 (42%), Positives = 147/248 (59%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M RY ++IEY G+ + GWQ Q  G SIQ  I+  +     E VV+ G+GRTD+GVHA+ Q
Sbjct: 1   MFRYQVLIEYIGTNFVGWQIQSKGKSIQKEIQVKLSKFLKEKVVLIGSGRTDAGVHAIEQ 60

Query: 61  VAHFDLVREWVPV-ILCKALNAYLKISDT-ISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            AHFD  +E   +  L K++N +  I+D  IS+L +     +FHAR SA +R Y Y I  
Sbjct: 61  SAHFDCKKEIQNLDKLLKSINHF--INDKGISVLAIKKRSLKFHARHSAKQRIYKYIIFN 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R +  +LEK R W I K LD E M+  A+ L+G  DF+TFR+  C A S I+T+    + 
Sbjct: 119 RLSKPSLEKERGWHIIKKLDIELMKKGAKKLLGTKDFSTFRASSCNAKSSIKTMKSVKIK 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           S    IEI+  ++SFL  Q+RS VGSLK + + KW     E  ++++ R  C P AP EG
Sbjct: 179 SKDGRIEIQFKSQSFLQQQVRSMVGSLKYLAENKWDLKKFEFVIKSKKRILCAPPAPAEG 238

Query: 239 LYFDSVEY 246
           L+ + V Y
Sbjct: 239 LFLEKVIY 246


>gi|114320390|ref|YP_742073.1| tRNA pseudouridine synthase A [Alkalilimnicola ehrlichii MLHE-1]
 gi|114226784|gb|ABI56583.1| tRNA pseudouridine synthase A [Alkalilimnicola ehrlichii MLHE-1]
          Length = 261

 Score =  189 bits (480), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 102/249 (40%), Positives = 142/249 (57%), Gaps = 12/249 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + +EY+GSG+ GWQRQ +  S+Q ++E A+  V  E V V  AGRTD+GVHA  QV 
Sbjct: 4   RFALGLEYDGSGFCGWQRQDHAPSVQAALEAALSRVADEPVTVTCAGRTDTGVHATGQVV 63

Query: 63  HFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HF+         WV       L A   + DT+S+  +  V + FHARF A+RRSY Y   
Sbjct: 64  HFETGAYRPEHAWV-------LGANANLPDTVSVHWVQPVSEAFHARFGALRRSYRYVWY 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             ++  AL +GR      +LD E M +AA HL+GRHDF+ FR++ CQA  P+R +   DV
Sbjct: 117 CSRSRPALLRGRVAWSKYALDPEPMAMAAGHLLGRHDFSAFRAVACQAKHPVRELYRLDV 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
            + G  + + V A +FLH  +R+  G+L L+G G+  +T     L   DR   G  AP E
Sbjct: 177 WARGGFVYLDVCANAFLHHMVRNLAGTLALIGRGERPATWAADLLAGGDRTRAGATAPAE 236

Query: 238 GLYFDSVEY 246
           GLY   V+Y
Sbjct: 237 GLYLVGVDY 245


>gi|254492043|ref|ZP_05105220.1| tRNA pseudouridine synthase A [Methylophaga thiooxidans DMS010]
 gi|224462740|gb|EEF79012.1| tRNA pseudouridine synthase A [Methylophaga thiooxydans DMS010]
          Length = 259

 Score =  187 bits (474), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 101/250 (40%), Positives = 140/250 (56%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY G+ + GWQ Q N  ++QG +EKA  +V    + V  AGRTD+GVHAL QV
Sbjct: 1   MRIALGIEYAGTDFCGWQNQPNTRTVQGELEKAASVVANHSIDVFAAGRTDTGVHALNQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       R W+       L     +   I++  +  VD +F+ARF+AI+R Y Y I
Sbjct: 61  VHFDTDAIRSERGWL-------LGINANLPKDINVAWMKPVDDEFNARFTAIKRRYRYLI 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           + R +  A+   R W     LD E M+ AA  LVG+HDF+ FR+  CQA SPI+T+D   
Sbjct: 114 LNRLSRSAVHHNRMWWHHHPLDIERMQAAADQLVGKHDFSAFRASECQARSPIKTLDKIT 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V    + I + V A+SFLH  +R+ VG +  +GDG          L++ DR + G  APP
Sbjct: 174 VRRQQDCIAVDVEAKSFLHHMVRNLVGVMAAIGDGSKPVDWAGDVLRSVDRSQGGVTAPP 233

Query: 237 EGLYFDSVEY 246
           +GLY   VEY
Sbjct: 234 QGLYLVDVEY 243


>gi|291614576|ref|YP_003524733.1| tRNA pseudouridine synthase A [Sideroxydans lithotrophicus ES-1]
 gi|291584688|gb|ADE12346.1| tRNA pseudouridine synthase A [Sideroxydans lithotrophicus ES-1]
          Length = 254

 Score =  187 bits (474), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 102/250 (40%), Positives = 147/250 (58%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GSGY GWQ Q +  +IQ +++ A+  + GE + +  AGRTD+GVHAL QV
Sbjct: 1   MRIALGIEYDGSGYNGWQSQPDVPNIQDTLQAALSRIAGENISIIAAGRTDTGVHALEQV 60

Query: 62  AHFD--LVR---EWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD  +VR    WV     +  NA L     +++L    V  +FHARFSA  RSY Y +
Sbjct: 61  VHFDTGIVRPLASWV-----RGTNALL--PKDVAVLWAHPVADEFHARFSAQARSYQYVL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           I R +  A+  G+       LD E MR+AAQ+L+G HDF+ FRS  CQA +P++T+   D
Sbjct: 114 INRPSRSAVHHGKVGWFHLPLDVEAMRMAAQNLLGEHDFSAFRSSQCQAKTPVKTLAQLD 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G++I   + A +FLH  +R+ VG L  VG GK+    + + LQ ++RK   P   P
Sbjct: 174 IVQQGDIIIFNLTANAFLHHMVRNIVGCLLYVGKGKYPPQWMHELLQGRERKLAAPTFAP 233

Query: 237 EGLYFDSVEY 246
           +GLY   + Y
Sbjct: 234 DGLYLCHITY 243


>gi|254447334|ref|ZP_05060801.1| tRNA pseudouridine synthase A [gamma proteobacterium HTCC5015]
 gi|198263473|gb|EDY87751.1| tRNA pseudouridine synthase A [gamma proteobacterium HTCC5015]
          Length = 261

 Score =  185 bits (470), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 143/250 (57%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EY+G+ Y GWQRQ NG S+Q  +E+++  V    V V  AGRTD+GVHA +QV
Sbjct: 1   MKIALGVEYDGTAYHGWQRQNNGISVQQVLEESLSKVANHGVQVQCAGRTDTGVHATQQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      +R W+       L A   +   +S+     V   FHARFSA  R Y Y I
Sbjct: 61  VHFESSAQRSIRNWI-------LGANANLPFDVSVRWAKQVSDDFHARFSAQGRRYRYLI 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           ++R +  AL   RA    K LD E M+ AAQHLVGRHDF+++R++HCQA SP+RT+   +
Sbjct: 114 LSRYSRSALWGRRATWTHKPLDLEVMQQAAQHLVGRHDFSSYRAVHCQAKSPVRTLHSLE 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+ I I V    FLH  +R+  G L  +G G+       + L+ +DR+  G  APP
Sbjct: 174 VGRAGDFIYIDVHGDGFLHHMVRNIAGVLMAIGAGEAVPDWSREVLEHRDRRLGGVTAPP 233

Query: 237 EGLYFDSVEY 246
            GLYF   EY
Sbjct: 234 WGLYFVHAEY 243


>gi|261855761|ref|YP_003263044.1| tRNA pseudouridine synthase A [Halothiobacillus neapolitanus c2]
 gi|261836230|gb|ACX95997.1| tRNA pseudouridine synthase A [Halothiobacillus neapolitanus c2]
          Length = 271

 Score =  185 bits (470), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 104/251 (41%), Positives = 139/251 (55%), Gaps = 12/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + +EY+GS Y GWQRQ    S+Q  +E A+  V    V V  AGRTD+GVHA  Q
Sbjct: 1   MARIALTLEYDGSRYHGWQRQSEVDSVQARLETALSRVADSPVDVVCAGRTDAGVHASHQ 60

Query: 61  VAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD       R W+       L     +   ISIL+   VD +FHARFSA  RSY Y 
Sbjct: 61  VVHFDTEAIRPERAWL-------LGVTQSLPSDISILSAQFVDPEFHARFSATARSYRYI 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I+ R    AL +GR       LD   M  A QHL+G HDF++FR+  CQ+ SP+R+I+  
Sbjct: 114 ILNRMTRSALHRGRITWWRGPLDESAMHEAGQHLLGEHDFSSFRAKDCQSVSPVRSIESL 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +++  G  + + + A +FLH  +R+ VG+L  VG G+  +  L   LQA+DR   G  AP
Sbjct: 174 NIHRQGEYVYMDITANAFLHHMVRNIVGTLLPVGAGERPADSLWDILQAKDRSAAGMTAP 233

Query: 236 PEGLYFDSVEY 246
            +GLY   V Y
Sbjct: 234 ADGLYLVGVRY 244


>gi|152996062|ref|YP_001340897.1| tRNA pseudouridine synthase A [Marinomonas sp. MWYL1]
 gi|150836986|gb|ABR70962.1| tRNA pseudouridine synthase A [Marinomonas sp. MWYL1]
          Length = 274

 Score =  183 bits (465), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 106/246 (43%), Positives = 148/246 (60%), Gaps = 5/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +  +++EYNGS Y GWQ QK G  S+Q ++EKA+ ++    V V  AGRTDSGVHA  QV
Sbjct: 4   KVVLVVEYNGSEYKGWQAQKFGVPSVQENLEKALAIIANHPVKVVCAGRTDSGVHASAQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            HF+   E         +N +L  SD I+++  S V   FHARFSA+ R Y Y I +   
Sbjct: 64  VHFETDVERNERAWTLGVNTHLP-SD-ITVVAASPVSNDFHARFSALSRRYRYVIYSSDF 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L KG  W   K+LD   M+ AA+  +G HDF++FR++ CQA +PIRTI +F+V+  
Sbjct: 122 CPAILSKGITWTY-KNLDVSAMKEAAKVFLGTHDFSSFRAVGCQAKTPIRTILNFEVHQL 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + V A +FLH  IR+F G L  +G G+   +  ++ L+A+DR + G  APP GLY
Sbjct: 181 GQYIVLDVRANAFLHHMIRNFAGVLMSIGAGEKPVSWAKQTLEAKDRTKGGITAPPTGLY 240

Query: 241 FDSVEY 246
           F   +Y
Sbjct: 241 FVDAQY 246


>gi|91776053|ref|YP_545809.1| tRNA pseudouridine synthase A [Methylobacillus flagellatus KT]
 gi|123254255|sp|Q1H0L9|TRUA_METFK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91710040|gb|ABE49968.1| tRNA pseudouridine synthase A [Methylobacillus flagellatus KT]
          Length = 261

 Score =  183 bits (464), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/245 (38%), Positives = 144/245 (58%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+G+ GWQ Q N  ++Q ++E A+  + G  V V  AGRTD+GVHAL QV
Sbjct: 1   MRLALGIEYDGAGFCGWQSQPNRLAVQDALESALSQLAGHQVRVSAAGRTDTGVHALSQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +N   K+   + +L    VD +FHARF A +RSY Y +I +  
Sbjct: 61  VHFDTEAVRSQTAWVRGVNT--KLPRGVRVLWAKEVDPRFHARFDAYQRSYQYWLINQPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G+A    + LD + M+ A  +L+G+HDF+ FR+  CQA SP++T+ H  V++FG
Sbjct: 119 APAVMAGKAGWFHQPLDLQAMQEAMAYLLGQHDFSAFRAAECQAKSPVKTMHHASVSAFG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +     A +FLH Q+R+ VG+L  +G GK+    + + L+ +DR+   P   P+GLY 
Sbjct: 179 SSMIFDFCASAFLHHQVRNMVGALVYIGKGKYPPVFIAELLEKRDRRCSPPTFSPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 TGVGY 243


>gi|58696853|ref|ZP_00372372.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           simulans]
 gi|58536935|gb|EAL60107.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           simulans]
          Length = 188

 Score =  182 bits (463), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 93/185 (50%), Positives = 125/185 (67%), Gaps = 2/185 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EYNGS + GWQ+Q++  +SIQ  IE AIF  +GE + ++  GRTD+GVHAL Q
Sbjct: 1   MRYKITVEYNGSSFSGWQKQQHSANSIQEKIENAIFNFSGEKIALYCGGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+ +E     +  A+N +LK S  I +LN  +VD  FHARFSA +R Y YRI+ R 
Sbjct: 61  VAHFDMEKECELYRIRNAINYHLK-SIPIVVLNAEVVDDAFHARFSAKKRYYEYRIVNRY 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           AP ALE G  W +   LD   MR AA+HL+G+HD ++FRS  C A++PIRTID  D+   
Sbjct: 120 APAALETGYVWQVFSPLDVNIMREAAKHLLGKHDLSSFRSKDCHAANPIRTIDDIDIVQN 179

Query: 181 GNLIE 185
           GN I+
Sbjct: 180 GNHIQ 184


>gi|291166165|gb|EFE28211.1| tRNA pseudouridine synthase A [Filifactor alocis ATCC 35896]
          Length = 244

 Score =  182 bits (461), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 97/241 (40%), Positives = 143/241 (59%), Gaps = 8/241 (3%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           I+Y G+ Y GWQ+Q NG SIQ  IE+AI  VTG+ V + G+GRTDSGVHAL QVA+F ++
Sbjct: 9   IQYIGTNYCGWQKQNNGKSIQQEIERAICEVTGKQVNLTGSGRTDSGVHALGQVANF-VI 67

Query: 68  REWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALE 126
              +PV   K A+N YL   D I I+    V+  FHAR+S+ +++Y YRI   +     E
Sbjct: 68  DTTIPVEKIKYAINYYL--PDDIRIIESKAVEDSFHARYSSKKKTYCYRINMNEIESPFE 125

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           K R++ + K LD   M+  ++ L+G HDF  F+S      + +RTI   ++N   N+ EI
Sbjct: 126 KNRSYFVGKELDLSKMKEQSKFLMGEHDFAAFQSEGSSVKTTVRTIYSLEINCINNIAEI 185

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGK-WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            ++   FL+  +R   G+L  +G GK ++  D+   L  + R+  GP AP  GL+ + VE
Sbjct: 186 HIIGNGFLYNMVRIIAGTLIEIGKGKDYSIVDI---LNTKQRENAGPTAPACGLFMEKVE 242

Query: 246 Y 246
           Y
Sbjct: 243 Y 243


>gi|296535340|ref|ZP_06897543.1| tRNA-pseudouridine synthase I [Roseomonas cervicalis ATCC 49957]
 gi|296264339|gb|EFH10761.1| tRNA-pseudouridine synthase I [Roseomonas cervicalis ATCC 49957]
          Length = 267

 Score =  181 bits (459), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 101/247 (40%), Positives = 146/247 (59%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIF-LVTGEIVVVHGAGRTDSGVHALR 59
           M RY +++E++G+ + GWQRQ +G S+Q  +E+A   L  G+      AGRTDSGVHA  
Sbjct: 15  MPRYALLVEFDGAPFVGWQRQPSGLSVQQVLEEAASPLNQGQPAATQAAGRTDSGVHAEG 74

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            V   D+ +   PV L +ALN Y      +++L +++   ++ ARFS I R+Y YRI+ R
Sbjct: 75  MVVQIDIAQALDPVRLREALN-YHTRPHPVAVLGVAVPPAEWSARFSCIGRAYRYRILNR 133

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +   AL+ GR W +  +LD   M  AAQ L+G+HDF+ FR+  CQA   +RT+D  DV  
Sbjct: 134 RPRPALQAGRVWHVGPALDAAAMHAAAQGLLGKHDFSAFRAASCQAKHALRTLDRLDVRR 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I   ARSFLH Q+R+ VG+L  VG G+       + L+A++R + G  AP EGL
Sbjct: 194 EGEEVVIHTAARSFLHHQVRNMVGTLAQVGLGRQGVDWPRRLLEARERSQAGQTAPAEGL 253

Query: 240 YFDSVEY 246
            F    Y
Sbjct: 254 TFLEARY 260


>gi|224825086|ref|ZP_03698192.1| tRNA pseudouridine synthase A [Lutiella nitroferrum 2002]
 gi|224602757|gb|EEG08934.1| tRNA pseudouridine synthase A [Lutiella nitroferrum 2002]
          Length = 262

 Score =  179 bits (455), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 140/245 (57%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G  + GWQ Q +G+++Q  +  A+  +    +    AGRTD+GVHAL QV
Sbjct: 1   MRVALGVEYDGRAFAGWQSQPHGNTVQDKLNLALSHIACAPINTVAAGRTDAGVHALMQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+  E       + +N++L     I+++    VD++FHARFSA  RSY Y ++T   
Sbjct: 61  VHFDVEVERPENAWVRGVNSHLPAD--IAVVWAKQVDEEFHARFSAFSRSYSYFLLTHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L  G+     + LD E MR AA HL+GRHDF++FR+  CQA SP++ +   D++   
Sbjct: 119 RSCLLAGKVGWYHQPLDVEAMREAAAHLLGRHDFSSFRAAECQAKSPVKHLQRLDIHEAD 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I   ++A +FLH  +R+ VG+L  VG G  +  D+   L A+DR+   P   P+GLY 
Sbjct: 179 GFIRFDLLADAFLHHMVRNIVGALVYVGKGTLSPEDMVDLLSARDRRHAPPTFMPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 TGVGY 243


>gi|226940175|ref|YP_002795248.1| tRNA pseudouridine synthase A [Laribacter hongkongensis HLHK9]
 gi|226715101|gb|ACO74239.1| TruA [Laribacter hongkongensis HLHK9]
          Length = 283

 Score =  179 bits (454), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 139/246 (56%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G G+ GWQRQ +  ++QG++E A+  + G  V V  AGRTD+GVHA +QV
Sbjct: 26  MRIALGLEYDGRGFAGWQRQPDQDTVQGALEGALSQIAGHPVSVLAAGRTDAGVHASQQV 85

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E       + +N +L     +++L +  V   FHARFSA  RSY Y ++    
Sbjct: 86  VHFDTGVERPLTAWVRGVNRFLPPG--VAVLWVQPVADDFHARFSACSRSYSYYLMNHPV 143

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL  GR       LD   M+ AA  L+G+HDF++FR+  CQA +P++T+  FD++   
Sbjct: 144 RPALGAGRVGWFHAPLDVPAMQAAAGLLLGQHDFSSFRAAECQAKTPVKTLARFDISEHD 203

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI   + A +FLH  +R+ VG+L  VG G      +   L A+DR +  P   P+GLY 
Sbjct: 204 GLIRFDLQADAFLHHMVRNLVGALVYVGKGAHAPEWMAGLLAARDRTQAPPTFMPDGLYL 263

Query: 242 DSVEYS 247
            +V Y 
Sbjct: 264 TAVGYP 269


>gi|289208514|ref|YP_003460580.1| tRNA pseudouridine synthase A [Thioalkalivibrio sp. K90mix]
 gi|288944145|gb|ADC71844.1| tRNA pseudouridine synthase A [Thioalkalivibrio sp. K90mix]
          Length = 269

 Score =  178 bits (452), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 103/249 (41%), Positives = 137/249 (55%), Gaps = 12/249 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + +EY+G G  GWQRQK+G S+QG +E A+  V  + V +  AGRTD+GVHA  QVA
Sbjct: 5   RWALGVEYDGRGLLGWQRQKDGPSVQGHLEAALSFVANDGVELTCAGRTDAGVHATAQVA 64

Query: 63  HFDL--VRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD   VRE   WV       L    ++ D I++     V+  FHARF A  R Y Y I 
Sbjct: 65  HFDTSAVRERHSWV-------LGVNSRLPDGIALRWAEPVNDDFHARFKACGRRYRYVIA 117

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R    ALE GR     + LD   M  AAQ  VG HDF++ R+  CQA SPIR +    V
Sbjct: 118 NRAVRPALEAGRVAWWRRPLDTARMHDAAQTFVGEHDFSSLRAAGCQAKSPIREVHSIAV 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ + + + A +FLH  +R+  G L  +GDG+       + L A+DR+  G  AP  
Sbjct: 178 QRRGSYVVLDIHANAFLHHMVRNIAGVLLAIGDGREEPGWAAQILAARDRRVSGITAPAG 237

Query: 238 GLYFDSVEY 246
           GLYF  V+Y
Sbjct: 238 GLYFVHVDY 246


>gi|157961443|ref|YP_001501477.1| tRNA pseudouridine synthase A [Shewanella pealeana ATCC 700345]
 gi|189030144|sp|A8H305|TRUA_SHEPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157846443|gb|ABV86942.1| tRNA pseudouridine synthase A [Shewanella pealeana ATCC 700345]
          Length = 261

 Score =  178 bits (452), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 96/247 (38%), Positives = 140/247 (56%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ    ++Q  +EKA+ +V  E + VH AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYDGSQYFGWQRQAEVDTVQERLEKALSIVANEPIAVHCAGRTDAGVHATGQV 60

Query: 62  AHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HF+   +R+     L   +N    + D I++  + +VD +FHARF+A  R Y Y I   
Sbjct: 61  VHFETNAIRKETAWTLGVNVN----LPDNIAVRWVKVVDDEFHARFTATARRYRYMIYNH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q    + +      P  +D   M  AAQ+L+G  DFT+FR++HCQ+++P R +   +V  
Sbjct: 117 QLRPGILRSGVSHYPGDIDESKMHQAAQYLLGEQDFTSFRAVHCQSNTPFRCVHEVNVTR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I + + A +FLH  +R+ VGSL  VG G  +   +E+ L  +DR +    A P GL
Sbjct: 177 QGMYICVDIKANAFLHHMVRNIVGSLLEVGLGNQSVEWIEQLLALKDRNKAAATAKPNGL 236

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 237 YLVDVTY 243


>gi|288941328|ref|YP_003443568.1| tRNA pseudouridine synthase A [Allochromatium vinosum DSM 180]
 gi|288896700|gb|ADC62536.1| tRNA pseudouridine synthase A [Allochromatium vinosum DSM 180]
          Length = 261

 Score =  178 bits (452), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 141/246 (57%), Gaps = 12/246 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M +EY+G+ + GWQ Q    ++Q  +E A+  V    V+VH AGRTD+GVHAL QV HF+
Sbjct: 1   MGVEYDGTHFHGWQTQSGVRTVQSELEAAVSRVANHPVIVHCAGRTDAGVHALEQVVHFE 60

Query: 66  LV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                  R WV       L A + +   + +     VD  FHARFSA  R Y Y+I+ R+
Sbjct: 61  TTATRSERSWV-------LGANVNLPPDVGVRWAHPVDDGFHARFSAQARHYRYQILARR 113

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +++ RA  + ++LD E MRIAA  LVG HDF++FR++ CQA SPIR + + D++  
Sbjct: 114 TRSPIQRDRAVWVHEALDLERMRIAAVALVGEHDFSSFRAVACQAKSPIRRVLYLDLSER 173

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
             LI + + A  FLH  +R+  G L  +G G+ +     + L+ +DR+  G  A P+GLY
Sbjct: 174 EGLITLAIGANGFLHHMVRNIAGVLMAIGRGEASVDWTRELLEVRDRRLGGVTAQPQGLY 233

Query: 241 FDSVEY 246
           F   +Y
Sbjct: 234 FVRADY 239


>gi|170727324|ref|YP_001761350.1| tRNA pseudouridine synthase A [Shewanella woodyi ATCC 51908]
 gi|238688683|sp|B1KKN8|TRUA_SHEWM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|169812671|gb|ACA87255.1| tRNA pseudouridine synthase A [Shewanella woodyi ATCC 51908]
          Length = 261

 Score =  178 bits (451), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ    S+Q  +E+A+  V  E + VH AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYDGSKYFGWQRQVEVDSVQAQLERALSKVANEPISVHCAGRTDTGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   + +       L   + + D I++    +VD+ FHARFSA  R Y Y I   Q 
Sbjct: 61  VHFDT--DAIRKESAWTLGVNVSLPDDIAVRWAKVVDEDFHARFSATARRYRYMIYNYQL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         LD   M  AAQH VG HDFT+FR++HCQ+ SP R +   +V   G
Sbjct: 119 RPGILRSGVSHYRTHLDENKMHEAAQHFVGEHDFTSFRALHCQSKSPNRNVHEVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+ VGSL  +G G  +   + + L  +DR +  P A P GLY 
Sbjct: 179 MYICVDIKANAFLHHMVRNIVGSLIEIGLGHQSHEWIPELLALKDRSKAAPTAKPNGLYM 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|330721742|gb|EGG99735.1| tRNA pseudouridine synthase A [gamma proteobacterium IMCC2047]
          Length = 269

 Score =  178 bits (451), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 98/247 (39%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           + R  + IEY+GSGY GWQ Q + S ++Q  +E A+  +    V V  AGRTD+GVHA  
Sbjct: 8   LTRVALGIEYHGSGYNGWQAQNHESITVQCELESALSKIADAPVRVFCAGRTDAGVHATG 67

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD+++        +  N +L   D+I +     V + FHARFSA+ R Y+Y I   
Sbjct: 68  QVVHFDVLKPRTENAWVRGTNTHL--PDSIRVRWAKFVPEDFHARFSAMARRYIYVIENT 125

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               A+         + LD E M++AA +LVG HDF+++R++ CQA S I+T+ H  V  
Sbjct: 126 PVHSAIMNKHFSFEDRPLDVERMQLAANYLVGEHDFSSYRTVRCQAKSAIKTVHHLKVER 185

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+LI I + A +FLH  +R+  G L +VG GK      ++ L A+DR   G  APP GL
Sbjct: 186 HGSLIAIDIYANAFLHHMVRNVAGVLMMVGMGKAEPVWAKQVLDARDRTVGGVTAPPNGL 245

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 246 YLVGVDY 252


>gi|82703035|ref|YP_412601.1| tRNA pseudouridine synthase A [Nitrosospira multiformis ATCC 25196]
 gi|82411100|gb|ABB75209.1| tRNA pseudouridine synthase A [Nitrosospira multiformis ATCC 25196]
          Length = 351

 Score =  178 bits (451), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 93/250 (37%), Positives = 138/250 (55%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  M++EY+GS + GWQ Q  G+++Q ++E A+  + GE + V  AGRTD+GVHA+ QV
Sbjct: 57  VRIAMVLEYDGSNFCGWQSQPGGNTVQDAVEAALSEIAGEAIRVVTAGRTDAGVHAIYQV 116

Query: 62  AHFDLVREWVPVILCKALNAYLK-----ISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD   E       + +NA+++     +   I++L  S     FHAR+ A+ R YLY +
Sbjct: 117 LHFDTRAE-------RPMNAWVRGANALLPSGIALLWASPTADDFHARYCALERCYLYLL 169

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           +       L + R       L  E+M++ AQ LVG HDF+ FR+  CQA SP+RT+   +
Sbjct: 170 LNHPVRPGLHQHRVGWYHHPLRLESMQMGAQMLVGEHDFSAFRAAACQAKSPVRTLTKLE 229

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   GN++   + A +FLH  +R+ VG L  VG GK+    + K L+   R E  P    
Sbjct: 230 VTRVGNMVAFELRANAFLHHMVRNIVGCLVYVGKGKFRPDWIGKLLENGKRSEAAPTFSA 289

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 290 SGLYLAGVAY 299


>gi|58699455|ref|ZP_00374196.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58534027|gb|EAL58285.1| tRNA pseudouridine synthase A [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 201

 Score =  177 bits (450), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 93/198 (46%), Positives = 121/198 (61%), Gaps = 1/198 (0%)

Query: 49  GRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAI 108
           GRTD+GVHAL QVAHFD+ +E     +  A+N +LK S  I +LN  +VD  FHARFSA 
Sbjct: 5   GRTDAGVHALGQVAHFDMEKECELYRIRNAINYHLK-SIPIVVLNAEVVDDAFHARFSAK 63

Query: 109 RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSP 168
           +R Y YRI+ R AP ALE G  W +   LD   MR AA+HL+G+HD ++FRS  C A++P
Sbjct: 64  KRYYEYRIVNRYAPAALETGYVWQVFSPLDVNIMREAAKHLLGKHDLSSFRSKDCHAANP 123

Query: 169 IRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK 228
           IRTID  D+   GN I I++ A SFLH Q+R   G+L   G  +    ++   L    R 
Sbjct: 124 IRTIDDIDIVQNGNHIHIKISAISFLHNQVRIIAGTLVEFGKNRTNPQEMLHILSQCKRS 183

Query: 229 ECGPLAPPEGLYFDSVEY 246
             G  APP GLY   ++Y
Sbjct: 184 AAGVTAPPFGLYLVKIDY 201


>gi|255604972|ref|XP_002538318.1| pseudouridylate synthase, putative [Ricinus communis]
 gi|223512770|gb|EEF24066.1| pseudouridylate synthase, putative [Ricinus communis]
          Length = 283

 Score =  177 bits (449), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 96/245 (39%), Positives = 138/245 (56%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+GS + GWQ Q +G+++Q  ++ A+  + G  V V  AGRTD+GVHAL QV
Sbjct: 25  MRVVLGLEYDGSRFCGWQSQPSGAAVQDCLQTALAQMAGHEVKVSAAGRTDAGVHALSQV 84

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD           + +NA+L     + +L  S VD +FHARFSA RRSY Y +     
Sbjct: 85  AHFDTAVTRPQNAWVRGVNAFLPTG--VRVLWASEVDVEFHARFSAERRSYQYVLQVSPV 142

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G+     + LD + MR AA  L+G HDF+ FR+  CQA +PI+ +   D+  F 
Sbjct: 143 APAVLSGKVGWYHRPLDLKAMRNAASILLGEHDFSAFRASECQAKTPIKHLIQADIRQFD 202

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N+I     A +FLH  +R+ VGSL  VG G+     +   L+ +DR+   P   P+GLY 
Sbjct: 203 NVILFEFTASAFLHHMVRNLVGSLVYVGKGEHPPEWMRTLLEQKDRRLAAPTFMPDGLYL 262

Query: 242 DSVEY 246
             V Y
Sbjct: 263 TGVHY 267


>gi|89093241|ref|ZP_01166191.1| tRNA-pseudouridine synthase I [Oceanospirillum sp. MED92]
 gi|89082537|gb|EAR61759.1| tRNA-pseudouridine synthase I [Oceanospirillum sp. MED92]
          Length = 283

 Score =  177 bits (449), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 102/252 (40%), Positives = 142/252 (56%), Gaps = 16/252 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG--SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           RY + +EY+G+ Y GWQ Q+ G   SIQ ++EKA+  +    V V  AGRTD+ V+A  Q
Sbjct: 23  RYALCVEYSGAEYRGWQIQREGDVPSIQATVEKALSKIANAPVSVICAGRTDARVNATYQ 82

Query: 61  VAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           + HFD       R WV       +     + D I+I     V + FHARFSA+ R Y Y 
Sbjct: 83  IIHFDSPVRRDERAWV-------MGTNTNLPDDIAIQWAKQVPESFHARFSALERRYRYL 135

Query: 116 IITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           I +    P  L KG  W   K +D   M+ A +HLVG HDFT++R++ CQA SP+RT+  
Sbjct: 136 IYSNPVKPAILPKGITWTY-KEMDVARMQEAVKHLVGEHDFTSYRAVGCQAHSPVRTVKE 194

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           F+V   G L+ + V A +FLH  IR+F G L  +G G+      ++ L A+DR++ G  A
Sbjct: 195 FNVYREGRLVILDVRANAFLHHMIRNFAGVLMTIGCGEAEPIWAKEVLDARDRRQGGVTA 254

Query: 235 PPEGLYFDSVEY 246
           PP GLYF   +Y
Sbjct: 255 PPFGLYFVDAKY 266


>gi|307266981|ref|ZP_07548497.1| tRNA pseudouridine synthase A [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306917966|gb|EFN48224.1| tRNA pseudouridine synthase A [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 244

 Score =  176 bits (447), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 93/242 (38%), Positives = 138/242 (57%), Gaps = 2/242 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            +++EY+G+ Y GWQ Q+N  ++Q  ++KAI  VTGE V + GA RTD+GVHAL QVA+F
Sbjct: 5   MIVVEYDGTNYHGWQYQENAVTVQEVLQKAIKKVTGEEVNLIGASRTDTGVHALYQVANF 64

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +     L  ALN+ L   D I ++    V+  FHAR+SA R+ Y Y I+ R+ P+ 
Sbjct: 65  RTNTKIPAEKLPYALNSVL--PDDIVVVQAKDVEDSFHARYSAKRKRYKYIILNRKFPMP 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   W I   L  E M+ AA +L+G HDF+ F++     +S IRT+    +      I
Sbjct: 123 TMRNYCWHISYPLSIEKMKKAASYLIGTHDFSAFKASGSSKTSTIRTVYDLTIEKNEEFI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FL+  +R  VG+L  VG GK    ++   L+++DR + G  APP+GLY   +
Sbjct: 183 NIEIEANGFLYNMVRIIVGTLSYVGLGKIEENEVYDILKSRDRTKAGITAPPQGLYLIKI 242

Query: 245 EY 246
            Y
Sbjct: 243 MY 244


>gi|302385211|ref|YP_003821033.1| tRNA pseudouridine synthase A [Clostridium saccharolyticum WM1]
 gi|302195839|gb|ADL03410.1| tRNA pseudouridine synthase A [Clostridium saccharolyticum WM1]
          Length = 248

 Score =  176 bits (446), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 94/249 (37%), Positives = 146/249 (58%), Gaps = 4/249 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           MI+ Y M++EY+GS Y GWQ+Q N   +IQG IE+ +  +TG+ V VHG+GRTD+GVHAL
Sbjct: 1   MIKNYRMVLEYDGSRYDGWQKQGNTEQTIQGKIEQVLERMTGQAVEVHGSGRTDAGVHAL 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QVA+F +  +     + + LN YL   + I ++ L    ++FH+R +A  ++YLYRI  
Sbjct: 61  AQVANFHMDGKMASKEIQEYLNQYL--PEDIRVITLEPAKERFHSRLNAQEKTYLYRIEM 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +     E+   + + KSL+ E M  A+ +L G HDF +F S      S +R +   +  
Sbjct: 119 GERKQVFERKYIYGLYKSLNVEAMERASAYLTGEHDFKSFCSNRKMKKSTVRVLKEIEFE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ + IR     FL+  +R   G+L  VG G+  + D++  L+A+DR + G  APPEG
Sbjct: 179 QQGSRLLIRYTGNGFLYNMVRIITGTLIEVGLGQRKAEDMKGILEAKDRNQAGFTAPPEG 238

Query: 239 LYFDSVEYS 247
           L+ + V Y+
Sbjct: 239 LFLEQVRYN 247


>gi|134094449|ref|YP_001099524.1| tRNA pseudouridine synthase A [Herminiimonas arsenicoxydans]
 gi|189030136|sp|A4G4G0|TRUA_HERAR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|133738352|emb|CAL61397.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA
           pseudouridylate synthase I) [Herminiimonas
           arsenicoxydans]
          Length = 275

 Score =  176 bits (446), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 141/246 (57%), Gaps = 2/246 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + ++Y+G+ + GWQ Q NG ++Q  +E A++  T + +    AGRTD+GVHAL QV 
Sbjct: 13  RIVLGVQYDGAPWQGWQTQLNGLTVQDKLEFALYKFTQQTITTACAGRTDAGVHALEQVV 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVD--KQFHARFSAIRRSYLYRIITRQ 120
           HFD   E       + +N +L  S  +   +    D  + FHARFSA  R+Y Y +    
Sbjct: 73  HFDTTLERDMQSWVRGVNTFLPSSIAVRWASEVAHDPAENFHARFSARSRTYHYMLYNNP 132

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               L +G+A  + ++LD   M+ AA HL+G+HDF+ FRS+ CQA SP++T+    +   
Sbjct: 133 VRSPLLEGKAGWVFRALDIAKMQEAAAHLLGQHDFSAFRSVQCQAKSPVKTMHAIKIERR 192

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+LI   V A +FLH  +R+ VGSL  VG+G    + L++ L  Q+RK   P   P+GLY
Sbjct: 193 GDLIMFTVHANAFLHHMVRNIVGSLIYVGNGTQAPSWLKEVLAGQERKFAAPTFMPDGLY 252

Query: 241 FDSVEY 246
              ++Y
Sbjct: 253 LAKIDY 258


>gi|167036834|ref|YP_001664412.1| tRNA pseudouridine synthase A [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167039553|ref|YP_001662538.1| tRNA pseudouridine synthase A [Thermoanaerobacter sp. X514]
 gi|256752665|ref|ZP_05493517.1| tRNA pseudouridine synthase A [Thermoanaerobacter ethanolicus
           CCSD1]
 gi|300915196|ref|ZP_07132511.1| tRNA pseudouridine synthase A [Thermoanaerobacter sp. X561]
 gi|307725120|ref|YP_003904871.1| tRNA pseudouridine synthase A [Thermoanaerobacter sp. X513]
 gi|320115256|ref|YP_004185415.1| tRNA pseudouridine synthase A [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|238687621|sp|B0K5S6|TRUA_THEPX RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238687718|sp|B0KCN3|TRUA_THEP3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166853793|gb|ABY92202.1| tRNA pseudouridine synthase A [Thermoanaerobacter sp. X514]
 gi|166855668|gb|ABY94076.1| tRNA pseudouridine synthase A [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|256748485|gb|EEU61537.1| tRNA pseudouridine synthase A [Thermoanaerobacter ethanolicus
           CCSD1]
 gi|300888920|gb|EFK84067.1| tRNA pseudouridine synthase A [Thermoanaerobacter sp. X561]
 gi|307582181|gb|ADN55580.1| tRNA pseudouridine synthase A [Thermoanaerobacter sp. X513]
 gi|319928347|gb|ADV79032.1| tRNA pseudouridine synthase A [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 244

 Score =  176 bits (446), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 140/246 (56%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    +++EY+G+ Y GWQ QKN  ++Q  ++KAI  VTGE V + GA RTD+GVHAL Q
Sbjct: 1   MRNVMIVVEYDGTNYHGWQYQKNAVTVQEVLQKAIKKVTGEEVNLIGASRTDTGVHALYQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F    +     L  ALN+ L   D I ++    V+  FHAR+SA R+ Y Y I+ R+
Sbjct: 61  VANFKTNTKIPAEKLPYALNSVL--PDDIVVVQAKDVEDSFHARYSAKRKRYKYIILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +   +   W I   L+ E M+ AA +L+G HDF+ F++     +S IRT+    +   
Sbjct: 119 FQMPTMRNYCWHISYPLNIEEMKKAASYLIGTHDFSAFKASGSSKTSTIRTVYDLTIEKN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I I + A  FL+  +R  VG+L  VG GK    ++   L+++DR + G  APP+GLY
Sbjct: 179 EDFINIEIEANGFLYNMVRIIVGTLSYVGLGKIKEDEVYDILKSKDRTKAGITAPPQGLY 238

Query: 241 FDSVEY 246
              + Y
Sbjct: 239 LIKIIY 244


>gi|149189278|ref|ZP_01867564.1| tRNA pseudouridine synthase A [Vibrio shilonii AK1]
 gi|148836837|gb|EDL53788.1| tRNA pseudouridine synthase A [Vibrio shilonii AK1]
          Length = 267

 Score =  175 bits (444), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 101/248 (40%), Positives = 144/248 (58%), Gaps = 8/248 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG+ Y+GWQRQ++ SS+Q  +EKA+ +V  + V V  AGRTD+GVH   QV
Sbjct: 1   MKVALGIEYNGANYYGWQRQRDVSSVQEELEKALSIVANQPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HF+  ++R+  P      +NA L     I++     V ++FHARFSA  R Y Y I   
Sbjct: 61  VHFESSVIRK--PAAWTMGVNANL--PKDIAVRWAKEVHEEFHARFSATARRYRYVIFNH 116

Query: 120 QA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
              P  L  G +      LD E M  A Q+L+G +DFT+FR++HCQ+ SP R I H +V+
Sbjct: 117 ALRPGILSSGIS-HYHGELDAEKMHQAGQYLLGENDFTSFRAVHCQSRSPWRNIMHLNVS 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  + I + A +F+H  +R+  GSL +VG G  +   +E  LQ +DRK  G  A  EG
Sbjct: 176 RHGPYVVIDIKANAFVHHMVRNITGSLIVVGKGDQSPEWIEWLLQQKDRKLAGATAKAEG 235

Query: 239 LYFDSVEY 246
           LY   V+Y
Sbjct: 236 LYLVDVDY 243


>gi|319779623|ref|YP_004130536.1| tRNA pseudouridine synthase A [Taylorella equigenitalis MCE9]
 gi|317109647|gb|ADU92393.1| tRNA pseudouridine synthase A [Taylorella equigenitalis MCE9]
          Length = 268

 Score =  175 bits (444), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 95/249 (38%), Positives = 144/249 (57%), Gaps = 12/249 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + I Y+G  + GWQ Q NG ++Q  +E A+   T   V    AGRTD+GVHAL QV 
Sbjct: 4   RVALGISYDGRDFQGWQTQPNGLTVQDKLEAALREFTRHQVSTICAGRTDTGVHALGQVV 63

Query: 63  HFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD      +  W+     + +N++L   D+I +    IV   F ARFSA+ R+Y+Y + 
Sbjct: 64  HFDTEVDRNLESWI-----RGVNSHLP--DSIRVRWSKIVPDSFSARFSAVSRTYVYLLR 116

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             +    +  GRA     +LD E+M IA + ++G HDFT+FRS  CQASSP+RT+D F +
Sbjct: 117 NERVMSPIWSGRAGWDFHNLDVESMNIAKEKMIGTHDFTSFRSSQCQASSPVRTLDLFKI 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           N+ G  I   + A  FLH  +R+ +G++  VG G+++ + +   ++A++R    P   P+
Sbjct: 177 NAEGPFIIFTLRANGFLHHMVRNLIGTILYVGMGRFSPSKIPDLIEAKNRMFTAPTFMPD 236

Query: 238 GLYFDSVEY 246
           GLYF  V+Y
Sbjct: 237 GLYFARVDY 245


>gi|218460354|ref|ZP_03500445.1| tRNA pseudouridine synthase A [Rhizobium etli Kim 5]
          Length = 141

 Score =  175 bits (444), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 78/119 (65%), Positives = 95/119 (79%)

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
           G+AW +PK+LD E M  AAQ LVGRHDF+TFRS HCQA+SP+RT+D  DV   G LIEIR
Sbjct: 2   GKAWWVPKTLDHEVMHAAAQRLVGRHDFSTFRSAHCQANSPVRTLDRLDVTRSGALIEIR 61

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             A+SFLH QIRSF G+LKL G+GKWT  D+E AL+A++RK CGP+APP+GLYF  V+Y
Sbjct: 62  ATAQSFLHNQIRSFAGTLKLAGEGKWTPDDVEAALEARNRKACGPVAPPDGLYFLQVDY 120


>gi|94498945|ref|ZP_01305483.1| tRNA pseudouridine synthase A [Oceanobacter sp. RED65]
 gi|94428577|gb|EAT13549.1| tRNA pseudouridine synthase A [Oceanobacter sp. RED65]
          Length = 297

 Score =  175 bits (444), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 102/252 (40%), Positives = 143/252 (56%), Gaps = 16/252 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           R+   +EYNG+ + GWQ+QK+  G S+Q ++EKAI  V    V V  AGRTD+GVHA  Q
Sbjct: 30  RFVAGVEYNGALFKGWQKQKHYAGPSVQEALEKAISRVANHTVDVVCAGRTDAGVHASAQ 89

Query: 61  VAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD       R W        L     + D + +  +    + FHARFSA+ R Y Y 
Sbjct: 90  VIHFDTSAVRDERAW-------KLGINTNLPDGVCVNWIMPAPQDFHARFSAVARRYRYF 142

Query: 116 IITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           I+ +Q  P  +  G +W   + LD E M  AAQ+L+G HDFT+FR+  CQA   +RT+ +
Sbjct: 143 IMNKQVKPGLMHDGVSWW-RRPLDAEKMHEAAQYLLGEHDFTSFRAKDCQARHAVRTMKY 201

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V    + + + V A +FL+  +R+ VG L  +G+GK      E+ L AQDR++ G  A
Sbjct: 202 ISVKRLNDWVIVEVCANAFLYHMVRNIVGVLLPIGEGKKPVEWCEQVLAAQDRRQAGVTA 261

Query: 235 PPEGLYFDSVEY 246
           P EGLYF +VEY
Sbjct: 262 PGEGLYFVNVEY 273


>gi|90021726|ref|YP_527553.1| pseudouridylate synthase [Saccharophagus degradans 2-40]
 gi|89951326|gb|ABD81341.1| tRNA pseudouridine synthase A [Saccharophagus degradans 2-40]
          Length = 289

 Score =  175 bits (444), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 100/252 (39%), Positives = 148/252 (58%), Gaps = 8/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + +EY+GS Y G+QRQ    +++Q  +EKA+  V  E V +  AGRTD+GVHA  
Sbjct: 22  MRRVVLQVEYDGSPYCGFQRQLTAPNTVQAELEKALSSVANEPVTIVCAGRTDAGVHATS 81

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q+ HFD +         + +N +L  S  I +++   V   FHARFSA+ R+Y Y I   
Sbjct: 82  QIVHFDTLAGRPSKAWLQGVNTHLPFS--IRVISAKEVGFDFHARFSALSRTYRYVIHVS 139

Query: 120 QAPLA-LEKGRAWL-IPKSL---DCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           Q   A L  G  W+ +P+ L   D   M+ AA  L+G HDFT+FR++HCQA+SP+RT++ 
Sbjct: 140 QVRSAHLVNGVTWVKLPQKLSGLDVPAMQEAASLLLGEHDFTSFRTVHCQAASPVRTMEV 199

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            DV   G  I ++V A +FLH  +R+ VG L  VG G+   + + + ++ +DR +    A
Sbjct: 200 ADVVQMGEFIVVQVTANAFLHHMVRNIVGVLLRVGRGELKPSRVTELIELRDRSQAAETA 259

Query: 235 PPEGLYFDSVEY 246
           P  GLYF +V+Y
Sbjct: 260 PAAGLYFVNVQY 271


>gi|220934425|ref|YP_002513324.1| tRNA pseudouridine synthase A [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995735|gb|ACL72337.1| tRNA pseudouridine synthase A [Thioalkalivibrio sp. HL-EbGR7]
          Length = 259

 Score =  175 bits (443), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 104/252 (41%), Positives = 136/252 (53%), Gaps = 14/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + +EY+GSG+ GWQ Q  G ++Q  +E+A+  V    V V  AGRTD+GVHA  Q
Sbjct: 1   MMRIALGVEYDGSGFCGWQTQLQGRAVQACVEQALSRVANHPVSVVCAGRTDAGVHATAQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD       R WV       L     +   IS+L    VD  F ARFSA  R Y Y 
Sbjct: 61  VIHFDTESVRTARSWV-------LGGNTHLPPEISLLWAKEVDADFSARFSARSRRYRYV 113

Query: 116 IITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           I+ R   P  L +  +W  P  LD E M  A Q L+G  DFT+FR++ CQA SP+RT+  
Sbjct: 114 ILNRWVRPGVLHRKVSWHHPP-LDAERMHAAGQRLLGEWDFTSFRAVGCQAKSPVRTLLS 172

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G+ I + V A +FLH  +R+  G L  VG+G+     + + L A+DR   G  A
Sbjct: 173 LSVTRRGDFIYLDVHANAFLHHMVRNIAGVLMAVGEGERPVEWVSEVLHARDRTLGGVTA 232

Query: 235 PPEGLYFDSVEY 246
           PP GLY   VEY
Sbjct: 233 PPHGLYLVHVEY 244


>gi|294789610|ref|ZP_06754844.1| tRNA pseudouridine synthase A [Simonsiella muelleri ATCC 29453]
 gi|294482411|gb|EFG30104.1| tRNA pseudouridine synthase A [Simonsiella muelleri ATCC 29453]
          Length = 261

 Score =  174 bits (442), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 93/252 (36%), Positives = 149/252 (59%), Gaps = 17/252 (6%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           RY + + YNGS ++GWQ+Q  +  ++Q ++E A+ ++  + + V  AGRTD+GVHA  QV
Sbjct: 4   RYVLTLAYNGSAFYGWQKQTADVPTVQSALEHALSVIAQQPIKVTAAGRTDTGVHATAQV 63

Query: 62  AHFD-----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      +  WV     + +NA+L   + +++L+   V  +FHARF A  R Y  R 
Sbjct: 64  VHFDSDANRPISAWV-----RGVNAHLP--NDVAVLHAQAVASEFHARFDAFARRY--RY 114

Query: 117 ITRQAPL--ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           + + AP+   L  GRA     +LD  N++ A Q L+G HDF++FR+  CQA SPI+T+  
Sbjct: 115 VLQFAPVRSPLLVGRAGWTHYNLDINNIQAACQFLLGEHDFSSFRAAECQAKSPIKTMYS 174

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            D+ + G+LI++   A +FLH  IR+ VG+L  VG G+ +  +  + ++ + R +  P  
Sbjct: 175 IDIQAMGDLIKLDFHANAFLHHMIRNIVGALVYVGSGRLSVNEFAELIEKRSRLDAPPTF 234

Query: 235 PPEGLYFDSVEY 246
            P+GLYF   +Y
Sbjct: 235 MPDGLYFAGADY 246


>gi|59712303|ref|YP_205079.1| tRNA pseudouridine synthase A [Vibrio fischeri ES114]
 gi|197334265|ref|YP_002156517.1| tRNA pseudouridine synthase A [Vibrio fischeri MJ11]
 gi|62901138|sp|Q5E455|TRUA_VIBF1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238690294|sp|B5FFN7|TRUA_VIBFM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|59480404|gb|AAW86191.1| pseudouridylate synthase I [Vibrio fischeri ES114]
 gi|197315755|gb|ACH65202.1| tRNA pseudouridine synthase A [Vibrio fischeri MJ11]
          Length = 262

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 99/246 (40%), Positives = 139/246 (56%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ++ +S+Q  +EKA+ +V  E + VH AGRTD+GVH   QV
Sbjct: 1   MRIALCIEYDGAEYYGWQRQRDVNSVQEELEKALTIVANEPIEVHCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HFD              NA L     I++     V++ FHARF+A  R Y Y I   R 
Sbjct: 61  VHFDTTSSRKLAAWMMGANANL--PKNIAVRWAKEVNEDFHARFTATARRYRYIIYNNRL 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +     +LD   M  A Q+L+G +DFT+FR++HCQ+ SP R + H  V   
Sbjct: 119 RPAILGHGVS-HYHDALDANLMHEAGQYLLGENDFTSFRAVHCQSRSPWRNLMHLKVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I + A +F+H  +R+  GSL  VG GK     ++  L+A+DRK  G  A  EGLY
Sbjct: 178 GDFIVIDIKANAFVHHMVRNITGSLIEVGKGKQKPEWIKWLLEAKDRKLAGATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVDVDY 243


>gi|88812707|ref|ZP_01127954.1| Pseudouridylate synthase [Nitrococcus mobilis Nb-231]
 gi|88790123|gb|EAR21243.1| Pseudouridylate synthase [Nitrococcus mobilis Nb-231]
          Length = 284

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 99/250 (39%), Positives = 140/250 (56%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS + GWQRQ +  S+Q ++E+A+  V    V V  AGRTD+GVHA  QV
Sbjct: 26  MRVALGIEYDGSRFSGWQRQSHRLSVQVALEEALSRVADHPVTVTCAGRTDAGVHATHQV 85

Query: 62  AHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD       R WV     + +N+ L     I I  +  V + FHARF+A  RSY Y I
Sbjct: 86  IHFDTTAPRPSRAWV-----RGVNSNLP--GDIRITWVRAVPQVFHARFAATARSYRYVI 138

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           ++R  P AL + R     + L    MR+AAQ+L+G HDF+++R++ CQA  P+RT+   D
Sbjct: 139 LSRAVPPALHRRRVAWTYRPLQLSAMRVAAQYLLGEHDFSSYRALACQARHPVRTVHRLD 198

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+   + V A +FLH  +R+  G L  +G G        + LQA+DR   G  AP 
Sbjct: 199 ITRCGDYFYVDVTANAFLHHMVRNIAGVLLSIGSGARPPQWSWEILQARDRTAGGVTAPA 258

Query: 237 EGLYFDSVEY 246
            GLY  +V Y
Sbjct: 259 GGLYLVAVRY 268


>gi|71280165|ref|YP_270466.1| tRNA pseudouridine synthase A [Colwellia psychrerythraea 34H]
 gi|123760979|sp|Q47XK4|TRUA_COLP3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|71145905|gb|AAZ26378.1| tRNA pseudouridine synthase A [Colwellia psychrerythraea 34H]
          Length = 259

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 144/245 (58%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +RY + IEY+G  Y GWQRQ N  ++Q  +EKA+  +  E + V  AGRTD+GV+A  QV
Sbjct: 1   MRYALGIEYDGKNYCGWQRQNNVITVQEKLEKALSKIADEKIEVVCAGRTDTGVNATNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD  ++         +N +L  SD +++  +  VD  FHARFSA  R+Y Y I  +  
Sbjct: 61  IHFDTEKKRKDTAWTLGVNTHLP-SD-VAVAWVKKVDDDFHARFSATARNYRYIIYNKPL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+          +LD   M+  A +L+G+HDFT+FR++HCQ+ S +RTI H  V   G
Sbjct: 119 RSAILSHGISHCHFALDENLMQQGADYLLGKHDFTSFRTVHCQSHSAVRTIKHCRVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + + + A +FLH  +R+ VGSL  VG  + T   +++ L A++R   G  APPEGLYF
Sbjct: 179 DYLVVDIKANAFLHHMVRNVVGSLMRVGQSQETPHWMKEVLLAKNRCVAGVTAPPEGLYF 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|253999257|ref|YP_003051320.1| tRNA pseudouridine synthase A [Methylovorus sp. SIP3-4]
 gi|253985936|gb|ACT50793.1| tRNA pseudouridine synthase A [Methylovorus sp. SIP3-4]
          Length = 261

 Score =  174 bits (440), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 93/250 (37%), Positives = 138/250 (55%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G+ + GWQ Q  G  +Q ++E+ +  +    V V  AGRTD+GVHAL QV
Sbjct: 1   MRVALGLEYDGAHFCGWQSQPGGCGVQDALERELARMACHPVRVIAAGRTDTGVHALAQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLK-----ISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+   E       + LNA+++     +  ++ +L    VD +FHARFSA +R Y Y +
Sbjct: 61  VHFETTTE-------RPLNAWVRGVNAGLPSSVRVLWAQQVDDEFHARFSARQRYYQYIL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             +    A+  G+     +SLD + M  AA HL+G HDF+ FR+  CQA SPIRT+   +
Sbjct: 114 FDQAVAPAILAGKVGWFHQSLDVDAMAEAAAHLIGEHDFSAFRAAECQAKSPIRTLQQAE 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  I       +FLH Q+R+ VG+L  VG G      +++ LQ+ DR+   P   P
Sbjct: 174 VRRAGQAILFEFSGNAFLHHQVRNMVGALVYVGKGSQPPAFIQQLLQSHDRRLAPPTFSP 233

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 234 DGLYLSGVGY 243


>gi|311086513|gb|ADP66594.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. TLW03
           (Acyrthosiphon pisum)]
          Length = 266

 Score =  174 bits (440), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 98/243 (40%), Positives = 139/243 (57%), Gaps = 2/243 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + +EY+GS Y GWQRQK   SIQ  IEKA+ ++    + V  AGRTD+GVH++ QV H
Sbjct: 9   FALGVEYDGSYYHGWQRQKIVPSIQEEIEKALSIIANHKIDVVCAGRTDAGVHSIGQVIH 68

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F              +N+YL  S+ IS++ +  V + FHAR+SAI RSY Y I       
Sbjct: 69  FKTTANRKKSSWSIGVNSYL--SENISVVWVKEVTENFHARYSAITRSYRYIIYNYSLRS 126

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+ + +   I + L+ + M   AQ L+G HDFT+FR++ CQ+ SP R I   +V  F N 
Sbjct: 127 AIFQTKLNHIYRKLNVDKMHFEAQFLLGEHDFTSFRALGCQSHSPWRNITKLNVFRFHNW 186

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A SFLH  +R+ VGSL  VG  K     ++  L+ +DR   G  AP +GLY   
Sbjct: 187 VVVDITANSFLHHMVRNIVGSLIEVGISKKKEYWIKDLLEKKDRSHAGATAPAKGLYLVY 246

Query: 244 VEY 246
           VEY
Sbjct: 247 VEY 249


>gi|219681571|ref|YP_002467957.1| pseudouridylate synthase I [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|219682129|ref|YP_002468513.1| pseudouridylate synthase I [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|257471256|ref|ZP_05635255.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. LSR1
           (Acyrthosiphon pisum)]
 gi|254789608|sp|B8D8Z8|TRUA_BUCA5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254789609|sp|B8D7A3|TRUA_BUCAT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|219621862|gb|ACL30018.1| pseudouridylate synthase I [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219624414|gb|ACL30569.1| pseudouridylate synthase I [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|311085941|gb|ADP66023.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. LL01
           (Acyrthosiphon pisum)]
 gi|311087094|gb|ADP67174.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
 gi|311087644|gb|ADP67723.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. JF98
           (Acyrthosiphon pisum)]
          Length = 266

 Score =  174 bits (440), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 98/243 (40%), Positives = 139/243 (57%), Gaps = 2/243 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + +EY+GS Y GWQRQK   SIQ  IEKA+ ++    + V  AGRTD+GVH++ QV H
Sbjct: 9   FALGVEYDGSYYHGWQRQKIVPSIQEEIEKALSIIANHKIDVVCAGRTDAGVHSIGQVIH 68

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F              +N+YL  S+ IS++ +  V + FHAR+SAI RSY Y I       
Sbjct: 69  FKTTANRKKSSWSIGVNSYL--SENISVVWVKEVTENFHARYSAITRSYRYIIYNYSLRS 126

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+ + +   I + L+ + M   AQ L+G HDFT+FR++ CQ+ SP R I   +V  F N 
Sbjct: 127 AIFQTKLNHIYRKLNVDKMHFEAQFLLGEHDFTSFRALGCQSHSPWRNITKLNVFRFHNW 186

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A SFLH  +R+ VGSL  VG  K     ++  L+ +DR   G  AP +GLY   
Sbjct: 187 VVVDITANSFLHHMVRNIVGSLIEVGISKKKEYWIKDLLEKKDRSHAGATAPAKGLYLVY 246

Query: 244 VEY 246
           VEY
Sbjct: 247 VEY 249


>gi|326390628|ref|ZP_08212183.1| tRNA pseudouridine synthase A [Thermoanaerobacter ethanolicus JW
           200]
 gi|325993306|gb|EGD51743.1| tRNA pseudouridine synthase A [Thermoanaerobacter ethanolicus JW
           200]
          Length = 244

 Score =  174 bits (440), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 93/242 (38%), Positives = 137/242 (56%), Gaps = 2/242 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            +++EY+G+ Y GWQ QKN  ++Q  ++KAI  VTGE V + GA RTD+GVHAL QVA+F
Sbjct: 5   MIVVEYDGTNYHGWQYQKNAVTVQEVLQKAIKKVTGEEVNLIGASRTDTGVHALYQVANF 64

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +     L  ALN+ L   D I ++    V+  FHAR+SA R+ Y Y I+ R+  + 
Sbjct: 65  KTNTKIPAEKLPYALNSVL--PDDIVVVQAKDVEDSFHARYSAKRKRYKYIILNRKFQMP 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   W I   L  E M+ AA +L+G HDF+ F++     +S IRT+    +    + I
Sbjct: 123 TMRNYCWHIDYPLSIEKMKKAASYLIGTHDFSAFKASGSSKTSTIRTVYDLTIEKDEDFI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FL+  +R  VG+L  VG GK    ++   L ++DR + G  APP+GLY   +
Sbjct: 183 NIEIEANGFLYNMVRIIVGTLSYVGLGKIEVNEVYDILTSRDRTKAGITAPPQGLYLIKI 242

Query: 245 EY 246
            Y
Sbjct: 243 MY 244


>gi|15616818|ref|NP_240030.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|11135207|sp|P57295|TRUA_BUCAI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|25292033|pir||D84953 pseudouridylate synthase (EC 4.2.1.70) [imported] - Buchnera sp.
           (strain APS)
 gi|10038881|dbj|BAB12916.1| pseudouridylate synthase I [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
          Length = 266

 Score =  174 bits (440), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 98/243 (40%), Positives = 139/243 (57%), Gaps = 2/243 (0%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           + + +EY+GS Y GWQRQK   SIQ  IEKA+ ++    + V  AGRTD+GVH++ QV H
Sbjct: 9   FALGVEYDGSYYHGWQRQKILPSIQEEIEKALSIIANHKIDVVCAGRTDAGVHSIGQVIH 68

Query: 64  FDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
           F              +N+YL  S+ IS++ +  V + FHAR+SAI RSY Y I       
Sbjct: 69  FKTTANRKKSSWSIGVNSYL--SENISVVWVKEVTENFHARYSAITRSYRYIIYNYSLRS 126

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNL 183
           A+ + +   I + L+ + M   AQ L+G HDFT+FR++ CQ+ SP R I   +V  F N 
Sbjct: 127 AIFQTKLNHIYRKLNVDKMNFEAQFLLGEHDFTSFRALGCQSHSPWRNITKLNVFRFHNW 186

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
           + + + A SFLH  +R+ VGSL  VG  K     ++  L+ +DR   G  AP +GLY   
Sbjct: 187 VVVDITANSFLHHMVRNIVGSLIEVGISKKKEYWIKDLLEKKDRSHAGATAPAKGLYLVY 246

Query: 244 VEY 246
           VEY
Sbjct: 247 VEY 249


>gi|149910526|ref|ZP_01899165.1| tRNA pseudouridine synthase A [Moritella sp. PE36]
 gi|149806369|gb|EDM66342.1| tRNA pseudouridine synthase A [Moritella sp. PE36]
          Length = 263

 Score =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 107/247 (43%), Positives = 138/247 (55%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS Y+GWQRQK+  S+Q  +E A+  V    V VH AGRTDSGVH   QV
Sbjct: 1   MRIALGIEYDGSKYYGWQRQKDVISVQEKLEDALSRVANHPVRVHCAGRTDSGVHGTGQV 60

Query: 62  AHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HFD   VR+ V   L   +NA L   D I++     VD++FHARFSA  R Y Y I   
Sbjct: 61  VHFDTDAVRQDVAWTL--GVNANL--PDDIAVRWALEVDEEFHARFSATARRYRYIIYNS 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q   A+           +D E M  AAQ LVG HDFT+FR+ HCQA SPI+T+ H +V  
Sbjct: 117 QLRPAILSAGVSHYYGDIDVELMHEAAQQLVGEHDFTSFRAKHCQAKSPIKTMHHINVIR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + I I V A +FLH  +R+  GSL  VG G    + + + L  +DR      +  EGL
Sbjct: 177 QNSYIIIDVKANAFLHHMVRNLAGSLMEVGKGNKPVSWIAELLAGKDRSVAAATSKAEGL 236

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 237 YMVEVDY 243


>gi|114331148|ref|YP_747370.1| tRNA pseudouridine synthase A [Nitrosomonas eutropha C91]
 gi|122313976|sp|Q0AGX7|TRUA_NITEC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|114308162|gb|ABI59405.1| tRNA pseudouridine synthase A [Nitrosomonas eutropha C91]
          Length = 277

 Score =  173 bits (438), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 95/250 (38%), Positives = 139/250 (55%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  +I+EY+G GY GWQ+Q +  S+Q  +E A+  +    + V  AGRTD+GVHAL QV
Sbjct: 1   MKIVLILEYDGRGYCGWQKQPDRISVQSRLESALSRIASSQIQVVAAGRTDAGVHALCQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      +  WV     +  NA L   D IS+L  S V+  FHARFSA  R+YLY +
Sbjct: 61  VHFETHVIRPLTAWV-----RGANALLP--DDISVLWASEVNDDFHARFSATERTYLYYL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           ++R A   + +G+      SLD E M+ AA+ L+G HDF+ FRS  CQA + IR +   D
Sbjct: 114 LSRPARPGIFQGKTGWTHYSLDLEKMQTAARFLIGEHDFSAFRSAECQAKNAIRKLVRLD 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           ++           A +FLH  +R+ +G+L  +G GK+    ++  L  +DR    P   P
Sbjct: 174 ISQSEQFFVFEFCANAFLHHMVRNILGALIYIGQGKYPPEWIQILLGKRDRTLAAPTFSP 233

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 234 DGLYLAGVRY 243


>gi|300703716|ref|YP_003745318.1| tRNA pseudouridylate synthase i [Ralstonia solanacearum CFBP2957]
 gi|299071379|emb|CBJ42698.1| tRNA pseudouridylate synthase I [Ralstonia solanacearum CFBP2957]
          Length = 274

 Score =  172 bits (437), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 98/252 (38%), Positives = 145/252 (57%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+G+ + GWQ Q +G+++Q  +E A+    G  +    AGRTD+GVHAL Q
Sbjct: 1   MTRIALGIQYDGAAFSGWQSQPHGNTVQDVLEAALRQFGGVELPTTVAGRTDAGVHALGQ 60

Query: 61  VAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII- 117
           + H D  LVRE  P    +  NA+L    T+++     V + FHARFSA RR+Y Y ++ 
Sbjct: 61  IVHLDTDLVRE--PFSWVRGTNAFLP--PTVAVRWAQAVPEDFHARFSAHRRTYYYALVS 116

Query: 118 --TRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
             TR   L  + G   L P +SLD   M+ AAQ LVG HDF++FR+  CQA SP++T+  
Sbjct: 117 GPTRSPLLGGKAGYVMLPPGQSLDVAAMQEAAQVLVGEHDFSSFRAAECQAKSPVKTLYS 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  + +R+   +FLH  +R+ +G L  +G G+  +  + + L A+DRK   P  
Sbjct: 177 AEVRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRRPAAWMAEVLAARDRKAAAPTF 236

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V Y
Sbjct: 237 MPDGLYLAEVGY 248


>gi|319760619|ref|YP_004124557.1| tRNA pseudouridine synthase A [Candidatus Blochmannia vafer str.
           BVAF]
 gi|318039333|gb|ADV33883.1| tRNA pseudouridine synthase A [Candidatus Blochmannia vafer str.
           BVAF]
          Length = 255

 Score =  172 bits (436), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 101/239 (42%), Positives = 137/239 (57%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y GWQ+QKNG S+Q  +E A+ +VT E V V  AGRTDSGVHAL QV HF+  
Sbjct: 8   IEYDGSRYCGWQKQKNGISVQDCVENALNIVTAESVSVFCAGRTDSGVHALGQVVHFETD 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
            ++        +N YL  S  I I  +S++ + FHARFSA+ R Y Y I   +   A+  
Sbjct: 68  VKYSKSAWTFGVNRYLPRS--ICIRWVSLMKQDFHARFSAVSRRYYYYIYNDKIRSAILF 125

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            + W   K LD   M  AAQ+L+G +DF+ FRS  CQ+ S  R + H  V   G  + I 
Sbjct: 126 QKTWHYTKLLDVCKMSRAAQYLLGENDFSAFRSAGCQSYSRCRNLYHLRVIRIGQCVIID 185

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A SFL+  +R+ VGSL  VG G   +  + + L++  R   G  AP +GLY   V+Y
Sbjct: 186 IQANSFLYRMVRNIVGSLVEVGCGNRPAIWILELLKSCKRSLAGMTAPADGLYLAEVKY 244


>gi|152980861|ref|YP_001353856.1| tRNA pseudouridine synthase A [Janthinobacterium sp. Marseille]
 gi|189029996|sp|A6T009|TRUA_JANMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|151280938|gb|ABR89348.1| tRNA pseudouridine synthase A [Janthinobacterium sp. Marseille]
          Length = 271

 Score =  172 bits (436), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 94/248 (37%), Positives = 137/248 (55%), Gaps = 4/248 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + ++Y+G+ + GWQ Q NG ++Q  +E A+   T + V    AGRTD+GVH L QV 
Sbjct: 7   RIVLGVQYDGTPWQGWQTQLNGLTVQDRLEFALSKFTLQTVSTVCAGRTDAGVHGLEQVV 66

Query: 63  HFDLVREWVPVILCKALNAYLKISDTI----SILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           HFD   E       + +N +L  S  +     + +       FHARFSA  R Y Y +  
Sbjct: 67  HFDTTLERDMSSWVRGVNTFLPPSIAVRWATEVAHNPDEQDNFHARFSARSRMYQYVLYN 126

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 L +G+A  + + LD E MR AAQHL+G HDF+TFRS+ CQA SP++++    + 
Sbjct: 127 NPVRSPLLEGKAGWVFRKLDVERMRTAAQHLLGEHDFSTFRSVQCQAKSPVKSMYSIKIE 186

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+LI   + A +FLH  +R+ VGSL  VG+G      L++ L  +DRK   P   P+G
Sbjct: 187 QRGDLIMFTLHANAFLHHMVRNIVGSLIYVGNGAQQPDWLKELLDGRDRKFAAPTFMPDG 246

Query: 239 LYFDSVEY 246
           LY   ++Y
Sbjct: 247 LYLAKIDY 254


>gi|284047733|ref|YP_003398072.1| tRNA pseudouridine synthase A [Acidaminococcus fermentans DSM
           20731]
 gi|283951954|gb|ADB46757.1| tRNA pseudouridine synthase A [Acidaminococcus fermentans DSM
           20731]
          Length = 245

 Score =  172 bits (435), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 135/247 (54%), Gaps = 3/247 (1%)

Query: 1   MIRYC-MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           MIR     + Y+G+ Y G+QRQKNG  +Q  +EKA+  V  E +++  AGRTD+GVHAL 
Sbjct: 1   MIRTIKATVAYDGTRYQGFQRQKNGVGVQQVLEKALTEVLKEPILIKAAGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV  F       P    +AL  +L     I+I    +V   FHARF A+ ++Y Y+I   
Sbjct: 61  QVISFATSSRIPPENYRRALEPHL--PPDIAIREAEVVRDDFHARFDAVDKTYQYKIYYS 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P   ++   W I + LD E M  AA  L+G+HDFT+F++   Q +SP+RT+       
Sbjct: 119 PLPDPTQRNTTWEIREKLDVEAMNRAAALLLGKHDFTSFKNQGSQDTSPVRTLTEAHWVQ 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GNL    +    FL+  +R+ VG L  VG G+W   D  + + A++RK+ G  AP +GL
Sbjct: 179 DGNLYTFTITGDGFLYRMVRNIVGCLVRVGTGQWNEEDFARVMAAKNRKQAGMAAPAQGL 238

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 239 YLMHVSY 245


>gi|325981656|ref|YP_004294058.1| tRNA pseudouridine synthase A [Nitrosomonas sp. AL212]
 gi|325531175|gb|ADZ25896.1| tRNA pseudouridine synthase A [Nitrosomonas sp. AL212]
          Length = 265

 Score =  172 bits (435), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 139/246 (56%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++EY+GS Y GWQ Q    SIQ ++E A+  +  E + V  AGRTD+GVHAL Q
Sbjct: 1   MARIILVLEYDGSRYCGWQSQPENCSIQNALETALSKIAHEEIHVITAGRTDAGVHALYQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +       + +NA+L   D I++L  S V  +FHAR+SA+ R YLY ++ + 
Sbjct: 61  VVHFDTFVQRPLNAWVRGVNAFLP--DDIAVLWASEVSDRFHARYSALERRYLYFLLNQS 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   +     + L  + M+ AA  L+G HDF++FR+  CQA SPIRTI    +   
Sbjct: 119 VRPGVNHKKVGWFHQPLQLDIMQRAANILIGEHDFSSFRAAACQAKSPIRTITQLKIARH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GNL+   + A +FL   +R+ +G L  +G GK++S  + + L+  +R    P   P GLY
Sbjct: 179 GNLLIFDLRANAFLQHMVRNIIGCLVYIGKGKYSSEWMLELLEGCNRAYAAPTFSPAGLY 238

Query: 241 FDSVEY 246
              V+Y
Sbjct: 239 LAGVKY 244


>gi|169347102|ref|ZP_02866044.1| tRNA pseudouridine synthase A [Clostridium perfringens C str.
           JGS1495]
 gi|169296785|gb|EDS78914.1| tRNA pseudouridine synthase A [Clostridium perfringens C str.
           JGS1495]
          Length = 244

 Score =  172 bits (435), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 93/241 (38%), Positives = 138/241 (57%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   VA+F 
Sbjct: 6   LIIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAYVANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       ALN+  K+   I I+N   V + FHAR+    ++Y Y I+ R+ P AL
Sbjct: 66  TNSNIPGKNFKAALNS--KLPKDIVIMNSEEVAEDFHARYMTTGKTYCYTILNREEPPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           E+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    + + GN I+
Sbjct: 124 ERNCVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIETEGNKIK 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL  + V 
Sbjct: 184 IYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKAGICVPPTGLCLEKVF 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|30248700|ref|NP_840770.1| tRNA pseudouridine synthase [Nitrosomonas europaea ATCC 19718]
 gi|42559793|sp|Q820P8|TRUA_NITEU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|30180295|emb|CAD84602.1| tRNA pseudouridine synthase [Nitrosomonas europaea ATCC 19718]
          Length = 272

 Score =  171 bits (434), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 91/251 (36%), Positives = 139/251 (55%), Gaps = 12/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            ++  + +EY+G GY GWQ+Q    S+Q  +E A+  V G  + V  AGRTD+GVHAL Q
Sbjct: 11  FVKIVLALEYDGRGYCGWQKQPGCLSVQSRLESALSGVAGRQIQVVAAGRTDAGVHALCQ 70

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDT-----ISILNLSIVDKQFHARFSAIRRSYLYR 115
           V H +         + + LNA+++ ++      ISIL  S V   FHARFSA  R+YLY 
Sbjct: 71  VVHLE-------TCVRRPLNAWIRGTNALLPGDISILEASEVSDDFHARFSATERTYLYY 123

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +++R A   +  G+   +   LD E M++AA+ L+G+HDF+ FRS  CQ+ + IR +   
Sbjct: 124 LLSRPARPGIHHGKIGWVHYPLDLEKMQMAAKLLIGKHDFSAFRSSECQSRTAIRQLTRL 183

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           +++    L      A +FLH  +R+ +G L  +G GK+    +   L+ +DR    P   
Sbjct: 184 NISQHQQLFVFEFCANAFLHHMVRNILGGLVYIGRGKYPPEWMRILLEKRDRTLAAPTFS 243

Query: 236 PEGLYFDSVEY 246
           P+GLY   V Y
Sbjct: 244 PDGLYLSGVRY 254


>gi|297545296|ref|YP_003677598.1| tRNA pseudouridine synthase A [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
 gi|296843071|gb|ADH61587.1| tRNA pseudouridine synthase A [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
          Length = 240

 Score =  171 bits (434), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 93/242 (38%), Positives = 137/242 (56%), Gaps = 2/242 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            ++++Y+G+ Y GWQ QKN  ++Q  ++KAI  VTGE V + GA RTD+GVHAL QVA+F
Sbjct: 1   MIVVQYDGTNYHGWQYQKNAITVQEVLQKAIKKVTGEEVNLIGASRTDTGVHALYQVANF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +     L  ALN+ L   D I I     V+  FHAR+SA R+ Y Y I+ R+  + 
Sbjct: 61  KTNTKIPAEKLPYALNSVL--PDDIVITQAKDVEDSFHARYSAKRKRYKYLILNRKFRMP 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   W I   L+ E M+ AA +L+G HDF+ F++     +S IRT+    +    + I
Sbjct: 119 TMRNYCWHISYPLNVEKMKKAATYLIGTHDFSAFKASGSSKTSTIRTVYDLIIEKNEDFI 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FL+  +R  VG+L  VG GK    ++   L ++DR + G  APP+GLY   +
Sbjct: 179 NIEIEADGFLYNMVRIIVGTLSYVGLGKIGENEVYNILASKDRTKAGITAPPQGLYLIKI 238

Query: 245 EY 246
            Y
Sbjct: 239 IY 240


>gi|85859802|ref|YP_462004.1| tRNA pseudouridine synthase A [Syntrophus aciditrophicus SB]
 gi|85722893|gb|ABC77836.1| tRNA pseudouridine synthase A [Syntrophus aciditrophicus SB]
          Length = 259

 Score =  171 bits (434), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 96/242 (39%), Positives = 139/242 (57%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++EY+G+ Y GWQRQ N  +IQ  +E++I  +T E V++HG+GRTD+GVHAL QVA+F 
Sbjct: 20  LVLEYDGTAYRGWQRQGNLPTIQKILEESIARITQEPVILHGSGRTDAGVHALNQVANFR 79

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    L + LN+ L     I I     VD++FH+R+SA  +SYLYRI+       L
Sbjct: 80  TSSRIPAANLLRGLNSLL--PGDIVIRETEDVDEEFHSRYSAKSKSYLYRILNSPVRSPL 137

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN-SFGNLI 184
           ++  AW I   LD E M  A   L G+HDFT+F +      S +RTI   ++      +I
Sbjct: 138 QRNSAWFIRCCLDLEKMAGAISLLCGKHDFTSFCAAGSDVKSCVRTIIRAEIERETEQVI 197

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I V A  FL   +R+ VG+L  +G G+ +S  +   L+A+DR   G  APP+GL+   V
Sbjct: 198 TISVEADGFLRHMVRNIVGTLVEIGAGQDSSEIMRDILEAKDRGCAGITAPPQGLFLQKV 257

Query: 245 EY 246
            Y
Sbjct: 258 SY 259


>gi|289579109|ref|YP_003477736.1| tRNA pseudouridine synthase A [Thermoanaerobacter italicus Ab9]
 gi|289528822|gb|ADD03174.1| tRNA pseudouridine synthase A [Thermoanaerobacter italicus Ab9]
          Length = 240

 Score =  171 bits (433), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 93/242 (38%), Positives = 137/242 (56%), Gaps = 2/242 (0%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            ++++Y+G+ Y GWQ QKN  ++Q  ++KAI  VTGE V + GA RTD+GVHAL QVA+F
Sbjct: 1   MIVVQYDGTNYHGWQLQKNAITVQEVLQKAIKKVTGEEVNLIGASRTDTGVHALYQVANF 60

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +     L  ALN+ L   D I I     V+  FHAR+SA R+ Y Y I+ R+  + 
Sbjct: 61  KTNTKMPAEKLPYALNSVL--PDDIVITQAKDVEDSFHARYSAKRKRYKYIILNRKFRMP 118

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +   W I   L+ E M+ AA +L+G HDF+ F++     +S IRT+    +    + I
Sbjct: 119 TMRNYCWHISYPLNVEKMKKAATYLIGTHDFSAFKASGSSKTSTIRTVYDLIIEKNEDFI 178

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FL+  +R  VG+L  VG GK    ++   L ++DR + G  APP+GLY   +
Sbjct: 179 NIEIEADGFLYNMVRIIVGTLSYVGLGKIGENEVYHILASKDRTKAGITAPPQGLYLIKI 238

Query: 245 EY 246
            Y
Sbjct: 239 IY 240


>gi|167573521|ref|ZP_02366395.1| tRNA pseudouridine synthase A [Burkholderia oklahomensis C6786]
          Length = 270

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQSQPHGKTVQDALERALAEFAQTSLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+S+     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTELDRADFSWVRGTNAFLP--STVSVQWAKPMPDTFHARFAAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  +   LD + MR AA+HLVG HDF+ FRS  CQA SPI+ +    +   G
Sbjct: 119 RSPMLAGRAGWVHMPLDVDAMREAAEHLVGEHDFSAFRSSECQAKSPIKHLYQISIRPDG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ ++ L + L ++DR    P   PEGLY 
Sbjct: 179 DFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPASWLAEVLDSRDRDCAAPTFMPEGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 AHVGY 243


>gi|167624561|ref|YP_001674855.1| tRNA pseudouridine synthase A [Shewanella halifaxensis HAW-EB4]
 gi|189030143|sp|B0TKZ4|TRUA_SHEHH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|167354583|gb|ABZ77196.1| tRNA pseudouridine synthase A [Shewanella halifaxensis HAW-EB4]
          Length = 261

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 138/247 (55%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ    ++Q  +EKA+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYDGSQYFGWQRQAEVDTVQERLEKALSIVANEPIAVQCAGRTDAGVHATGQV 60

Query: 62  AHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HF+   VR+     L   +N    + D I++  + +VD +FHARF+A  R Y Y I   
Sbjct: 61  VHFETNAVRKDTAWTLGVNVN----LPDNIAVRWVKVVDDEFHARFTATARRYRYMIYNH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q    + +      P  +D   M  AAQ+L+G  DFT+FR++ CQ+++P R +   +V+ 
Sbjct: 117 QLRPGILRSGVSHYPGVIDEAKMHQAAQYLLGEQDFTSFRAVQCQSNTPFRCVHEVNVSR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I + + A +FLH  +R+ VGSL  VG G      +E+ L  +DR +    A P GL
Sbjct: 177 QGMYICVDIKANAFLHHMVRNIVGSLLEVGLGNQPIEWIEQLLALKDRNKAAATAKPNGL 236

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 237 YLVDVTY 243


>gi|110799502|ref|YP_697060.1| tRNA pseudouridine synthase A [Clostridium perfringens ATCC 13124]
 gi|168205200|ref|ZP_02631205.1| tRNA pseudouridine synthase A [Clostridium perfringens E str.
           JGS1987]
 gi|168211871|ref|ZP_02637496.1| tRNA pseudouridine synthase A [Clostridium perfringens B str. ATCC
           3626]
 gi|110674149|gb|ABG83136.1| tRNA pseudouridine synthase A [Clostridium perfringens ATCC 13124]
 gi|170663322|gb|EDT16005.1| tRNA pseudouridine synthase A [Clostridium perfringens E str.
           JGS1987]
 gi|170710156|gb|EDT22338.1| tRNA pseudouridine synthase A [Clostridium perfringens B str. ATCC
           3626]
          Length = 244

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 92/241 (38%), Positives = 137/241 (56%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   VA+F 
Sbjct: 6   LTIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAYVANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       ALN+  K+   I I+N   V + FHAR+    ++Y Y I+ R+ P AL
Sbjct: 66  TNSNIPGKNFKAALNS--KLPKDIVIMNSEEVAEDFHARYMTTGKTYCYTILNREEPPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           E+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    + + GN I+
Sbjct: 124 ERNYVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIETEGNKIK 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL  + V 
Sbjct: 184 IYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKAGICVPPTGLCLEKVF 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|53722721|ref|YP_111706.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei K96243]
 gi|124382508|ref|YP_001025653.1| tRNA pseudouridine synthase A [Burkholderia mallei NCTC 10229]
 gi|126446203|ref|YP_001077728.1| tRNA pseudouridine synthase A [Burkholderia mallei NCTC 10247]
 gi|217422201|ref|ZP_03453704.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 576]
 gi|238563050|ref|ZP_04610365.1| tRNA pseudouridine synthase A [Burkholderia mallei GB8 horse 4]
 gi|251766902|ref|ZP_04819864.1| tRNA pseudouridine synthase A [Burkholderia mallei PRL-20]
 gi|254176501|ref|ZP_04883159.1| tRNA pseudouridine synthase A [Burkholderia mallei ATCC 10399]
 gi|254184999|ref|ZP_04891588.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1655]
 gi|254201168|ref|ZP_04907533.1| tRNA pseudouridine synthase A [Burkholderia mallei FMH]
 gi|254205140|ref|ZP_04911493.1| tRNA pseudouridine synthase A [Burkholderia mallei JHU]
 gi|62901261|sp|Q63JL6|TRUA_BURPS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228683|sp|A3MBU2|TRUA_BURM7 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228684|sp|A2S134|TRUA_BURM9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|52213135|emb|CAH39174.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei K96243]
 gi|126239057|gb|ABO02169.1| tRNA pseudouridine synthase A [Burkholderia mallei NCTC 10247]
 gi|147748780|gb|EDK55855.1| tRNA pseudouridine synthase A [Burkholderia mallei FMH]
 gi|147754726|gb|EDK61790.1| tRNA pseudouridine synthase A [Burkholderia mallei JHU]
 gi|160697543|gb|EDP87513.1| tRNA pseudouridine synthase A [Burkholderia mallei ATCC 10399]
 gi|184215591|gb|EDU12572.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1655]
 gi|217394432|gb|EEC34451.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 576]
 gi|238521484|gb|EEP84935.1| tRNA pseudouridine synthase A [Burkholderia mallei GB8 horse 4]
 gi|243064541|gb|EES46727.1| tRNA pseudouridine synthase A [Burkholderia mallei PRL-20]
 gi|261826841|gb|ABM98766.2| tRNA pseudouridine synthase A [Burkholderia mallei NCTC 10229]
          Length = 271

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + I+Y+G+ + GWQ Q +G ++Q ++E+++       +    AGRTD+GVH L Q
Sbjct: 1   MMRIALGIQYDGAAFCGWQSQPHGKTVQDALERSLAEFAQTSLHTTVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +       +  NA+L    T+++     +   FHARF+A  R+Y Y +    
Sbjct: 61  VVHFDTDLDRADFSWVRGTNAFLP--PTVAVQWAKPMPDTFHARFAAFERTYYYALYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +  GRA  +   LD + MR AA HLVG HDF+ FRS  CQA SP++ +    +   
Sbjct: 119 VRSPMLAGRAGWVHTPLDVDAMREAAAHLVGEHDFSAFRSSECQAKSPVKHLYQIGIRPD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I  R  A +FLH  +R+ +G L  VG G++ S+ L + L+++DR    P   PEGLY
Sbjct: 179 GDFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPSSWLAEVLESRDRDCAAPTFMPEGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAHVGY 244


>gi|326795335|ref|YP_004313155.1| tRNA pseudouridine synthase A [Marinomonas mediterranea MMB-1]
 gi|326546099|gb|ADZ91319.1| tRNA pseudouridine synthase A [Marinomonas mediterranea MMB-1]
          Length = 270

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 98/246 (39%), Positives = 140/246 (56%), Gaps = 5/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +  +++EY+GS Y GWQ QK +  ++Q  +E A+  +    V V  AGRTD+GVHA  QV
Sbjct: 5   KVVLVVEYDGSRYKGWQAQKFDVDTVQEKLEYALSKIANHSVGVICAGRTDAGVHASSQV 64

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            HF+   E         +N +L     IS++  + V  +FHARFSA+ R Y Y I   + 
Sbjct: 65  VHFETASERPIRAWTLGVNTHL--PPDISVVAANYVADEFHARFSALTRRYRYVIYQSEF 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  + KG  W   K L  + M+ AA   +G HDF+++R+I CQA SPIRT+ +F VN F
Sbjct: 123 RPAIMAKGVTWTY-KDLSEQKMQQAAACFIGTHDFSSYRAIGCQARSPIRTVLNFSVNKF 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +FLH  IR+F G L  +G G+      ++ L A+DR + G  APP GLY
Sbjct: 182 GQYIVLDIRANAFLHHMIRNFAGVLMAIGAGEKPVQWAKQVLDAKDRTQGGVTAPPHGLY 241

Query: 241 FDSVEY 246
           F   +Y
Sbjct: 242 FVDAQY 247


>gi|27365335|ref|NP_760863.1| tRNA pseudouridine synthase A [Vibrio vulnificus CMCP6]
 gi|37680609|ref|NP_935218.1| tRNA pseudouridine synthase A [Vibrio vulnificus YJ016]
 gi|320155720|ref|YP_004188099.1| tRNA pseudouridine synthase A [Vibrio vulnificus MO6-24/O]
 gi|31340462|sp|Q8CWK3|TRUA_VIBVU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|42559737|sp|Q7M7J4|TRUA_VIBVY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|27361482|gb|AAO10390.1| tRNA pseudouridine synthase A [Vibrio vulnificus CMCP6]
 gi|37199357|dbj|BAC95189.1| tRNA pseudouridine synthase A [Vibrio vulnificus YJ016]
 gi|319931032|gb|ADV85896.1| tRNA pseudouridine synthase A [Vibrio vulnificus MO6-24/O]
          Length = 264

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 97/245 (39%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ YFGWQRQ+  +S+Q  +EKA+  V    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTDYFGWQRQREVASVQEKLEKALSKVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNVERKMVAWTMGANANL--PKDIAVRWAKAVPDEFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q+L+G +DFT+FR++ CQ+ SP R + H +V   G
Sbjct: 119 RPGILGSGVSHYHGELDEKKMHEAGQYLLGENDFTSFRAVQCQSLSPFRNMIHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL +VG G+     ++  L+A+DRK  GP A  EGLY 
Sbjct: 179 HYVVIDIKANAFVHHMVRNITGSLIMVGRGEQDPEWIKWLLEAKDRKLAGPTAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|167566409|ref|ZP_02359325.1| tRNA pseudouridine synthase A [Burkholderia oklahomensis EO147]
          Length = 270

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQSQPHGKTVQDALERALAEFAQTSLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+S+     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTELDRADFSWVRGTNAFLP--STVSVQWAKPMPDTFHARFAAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  +   LD + MR AA+HLVG HDF+ FRS  CQA SPI+ +    +   G
Sbjct: 119 RSPMLAGRAGWVHMPLDVDAMREAAEHLVGEHDFSAFRSSECQAKSPIKHLYQIGIRPDG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ ++ L + L ++DR    P   PEGLY 
Sbjct: 179 DFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPASWLAEVLDSRDRDCAAPTFMPEGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 AHVGY 243


>gi|329900760|ref|ZP_08272580.1| tRNA pseudouridine synthase A [Oxalobacteraceae bacterium IMCC9480]
 gi|327549402|gb|EGF33969.1| tRNA pseudouridine synthase A [Oxalobacteraceae bacterium IMCC9480]
          Length = 267

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 92/252 (36%), Positives = 140/252 (55%), Gaps = 12/252 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + ++Y+G+ + GWQ Q +G+++Q  +++A+F  T   +  H AGRTD+GVHA+ QV 
Sbjct: 5   RLVLGVQYDGTPWHGWQTQLSGNTVQDRLQQALFKFTQSDITTHCAGRTDTGVHAIEQVV 64

Query: 63  HFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQ--FHARFSAIRRSYLYR 115
           HFD      +  WV     + LN +L  S  +    ++ +D Q  FHARFSA  R+Y Y 
Sbjct: 65  HFDTPLDRPISSWV-----RGLNTHLPPSIAVRWATVARLDPQHEFHARFSARSRTYHYL 119

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +        L   +A  + + LD + MR AAQ L+G HDFT FRS  CQA SP++ +   
Sbjct: 120 LYNNPVRSPLWNDKAGWVFRPLDLDRMREAAQSLIGTHDFTAFRSADCQAKSPVKMMHEI 179

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            +    +LI I++ A +FLH  +R+ VGSL  VG G+     L + +  +DR    P   
Sbjct: 180 AITRRDDLIVIKLHANAFLHHMVRNLVGSLIYVGTGRQPVDWLSELILQKDRHLAAPTFS 239

Query: 236 PEGLYFDSVEYS 247
           P+GLY   ++Y 
Sbjct: 240 PDGLYLAKIDYD 251


>gi|168216665|ref|ZP_02642290.1| tRNA pseudouridine synthase A [Clostridium perfringens NCTC 8239]
 gi|182381201|gb|EDT78680.1| tRNA pseudouridine synthase A [Clostridium perfringens NCTC 8239]
          Length = 244

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 92/241 (38%), Positives = 137/241 (56%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   VA+F 
Sbjct: 6   LTIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAYVANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       ALN+  K+   I I+N   V + FHAR+    ++Y Y I+ R+ P AL
Sbjct: 66  TNSNIPGKNFKAALNS--KLPKDIVIMNSEEVAEDFHARYMTTGKTYCYTILNREEPPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           E+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    + + GN I+
Sbjct: 124 ERNYVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIETEGNKIK 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL  + V 
Sbjct: 184 IYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKSGICVPPTGLCLEKVF 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|18311353|ref|NP_563287.1| tRNA pseudouridine synthase A [Clostridium perfringens str. 13]
 gi|42559846|sp|Q8XHV5|TRUA2_CLOPE RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|18146037|dbj|BAB82077.1| tRNA-pseudouridine synthase I [Clostridium perfringens str. 13]
          Length = 244

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 92/241 (38%), Positives = 137/241 (56%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   VA+F 
Sbjct: 6   LTIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAYVANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       ALN+  K+   I I+N   V + FHAR+    ++Y Y I+ R+ P AL
Sbjct: 66  TNSNIPGKNFKAALNS--KLPKDIVIINSEEVAEDFHARYMTTGKTYCYTILNREEPPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           E+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    + + GN I+
Sbjct: 124 ERNYVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIETEGNKIK 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL  + V 
Sbjct: 184 IYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKAGICVPPTGLCLEKVF 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|260773232|ref|ZP_05882148.1| tRNA pseudouridine synthase A [Vibrio metschnikovii CIP 69.14]
 gi|260612371|gb|EEX37574.1| tRNA pseudouridine synthase A [Vibrio metschnikovii CIP 69.14]
          Length = 264

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 98/246 (39%), Positives = 139/246 (56%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ YFGWQRQ++  S+Q  +EKA+ ++    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYFGWQRQRDVISVQEKLEKALSIIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            HFD   E          NA L     I++    +V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERNMAAWTMGANANL--PKDIAVRWAKVVADDFHARFSATARRYRYVIYNHAY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +   P+ LD + M++A Q+L+G +DFT+FR++HCQ+ SP R I H +V+  
Sbjct: 119 RPGILSSGVSHYHPE-LDVQRMQLAGQYLLGENDFTSFRAVHCQSRSPWRNIMHLNVSRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + + + A +F+H  +R+ VGSL  VG G+     +E  L A+DRK     A  EGLY
Sbjct: 178 ERYVVVDIKANAFVHHMVRNIVGSLIEVGRGEKEPQWIEWLLAAKDRKLAAATAKAEGLY 237

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 238 LVAVDY 243


>gi|83748092|ref|ZP_00945121.1| tRNA pseudouridine synthase A [Ralstonia solanacearum UW551]
 gi|207742812|ref|YP_002259204.1| trna pseudouridine synthase a (trna-uridine isomerasei) (trna
           pseudouridylate synthaseI protein [Ralstonia
           solanacearum IPO1609]
 gi|83725278|gb|EAP72427.1| tRNA pseudouridine synthase A [Ralstonia solanacearum UW551]
 gi|206594206|emb|CAQ61133.1| trna pseudouridine synthase a (trna-uridine isomerasei) (trna
           pseudouridylate synthaseI protein [Ralstonia
           solanacearum IPO1609]
          Length = 274

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 97/252 (38%), Positives = 143/252 (56%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+G+ + GWQ Q +G+++Q  +E A+    G  +    AGRTD+GVHAL Q
Sbjct: 1   MTRIALGIQYDGAAFSGWQSQPHGNTVQDVLEAALRQFGGVELPTTVAGRTDAGVHALGQ 60

Query: 61  VAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII- 117
           + H D  LVRE  P    +  NA+L    T+++     V + FHARFSA RR+Y Y ++ 
Sbjct: 61  IVHLDTDLVRE--PFSWVRGTNAFLP--STVAVRWAQAVPEDFHARFSAHRRTYYYALVS 116

Query: 118 --TRQAPLALEKGRAWLIPKS-LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
             TR   L  + G   L P   LD   M+ AAQ LVG HDF++FR+  CQA SP++T+  
Sbjct: 117 GPTRSPLLGGKAGYVMLPPGEWLDVAAMQEAAQVLVGEHDFSSFRAAECQAKSPVKTLYS 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  + +R+   +FLH  +R+ +G L  +G G+  +  + + L A+DRK   P  
Sbjct: 177 AEVRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRRPAAWMAEVLAARDRKAAAPTF 236

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V Y
Sbjct: 237 MPDGLYLAEVGY 248


>gi|209694634|ref|YP_002262562.1| tRNA pseudouridine synthase A [Aliivibrio salmonicida LFI1238]
 gi|238057726|sp|B6EIW6|TRUA_ALISL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|208008585|emb|CAQ78760.1| tRNA pseudouridine synthase A [Aliivibrio salmonicida LFI1238]
          Length = 262

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 100/248 (40%), Positives = 146/248 (58%), Gaps = 8/248 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y GWQ QK+ +S+Q  +EKA+ +V  E + V  AGRTD+GVH   QV
Sbjct: 1   MRIALCIEYDGASYHGWQSQKDVTSVQEELEKALMVVANEPIEVMCAGRTDAGVHGTGQV 60

Query: 62  AHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT- 118
            HFD   VR+ +PV +   +NA L     I++  +  V++ FHARF+A  R Y Y I   
Sbjct: 61  VHFDTNSVRK-LPVWMV-GVNANL--PKNIAVRWVKEVNEDFHARFTATARRYRYIIFNN 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           RQ P     G +    ++LD + M  A Q+L+G +DFT+FR++ CQ+ +P R + H  V 
Sbjct: 117 RQRPAIFSHGVS-HYHETLDADLMHEAGQYLLGENDFTSFRAVRCQSRTPWRNLIHLKVT 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I I + A +F+H  +R+  GSL  VG GK     ++  L+A+DRK  G  A  EG
Sbjct: 176 RHGDFIVIDIKANAFVHHMVRNITGSLIEVGRGKQKPEWVQWLLEAKDRKLAGATAKAEG 235

Query: 239 LYFDSVEY 246
           LY   V+Y
Sbjct: 236 LYLIDVDY 243


>gi|307825597|ref|ZP_07655815.1| tRNA pseudouridine synthase A [Methylobacter tundripaludum SV96]
 gi|307733483|gb|EFO04342.1| tRNA pseudouridine synthase A [Methylobacter tundripaludum SV96]
          Length = 267

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 100/251 (39%), Positives = 137/251 (54%), Gaps = 12/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+GSG+ GWQ Q +  S+Q  +E+A+  V    V V  AGRTD+GVHAL Q
Sbjct: 1   MTRIVLGIEYDGSGFSGWQWQTHQRSVQQVLEQALSKVANHPVTVQCAGRTDTGVHALEQ 60

Query: 61  VAHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD   E     WV       L     + D + I  +      FHAR+SAI R Y Y 
Sbjct: 61  VVHFDAKVERELHTWV-------LGGNSNLPDDVRITWVKPAVGDFHARYSAIARFYRYV 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I+ R    AL + +A      LD + M  AAQHL+G+HDF+TFR+  CQ+ SP R +   
Sbjct: 114 ILNRPIKSALLRNQATWHHNPLDADKMHRAAQHLIGKHDFSTFRAQGCQSKSPCREMYFI 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           DV    + + I + A +FLH  +R+  G L  +G GK   +  ++ L+ ++RK  G  AP
Sbjct: 174 DVYRDDDKVIIDISANAFLHHMVRNIAGVLMDIGAGKQDESWTQELLEVKNRKLGGVTAP 233

Query: 236 PEGLYFDSVEY 246
           P GLY  +V Y
Sbjct: 234 PYGLYLGAVYY 244


>gi|207722996|ref|YP_002253419.1| trna pseudouridine synthase a (trna-uridine isomerasei) (trna
           pseudouridylate synthaseI protein [Ralstonia
           solanacearum MolK2]
 gi|206588185|emb|CAQ18754.1| trna pseudouridine synthase a (trna-uridine isomerasei) (trna
           pseudouridylate synthaseI protein [Ralstonia
           solanacearum MolK2]
          Length = 274

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 99/255 (38%), Positives = 146/255 (57%), Gaps = 16/255 (6%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+G+ + GWQ Q +G+++Q  +E A+    G  +    AGRTD+GVHAL Q
Sbjct: 1   MTRIALGIQYDGAAFSGWQSQPHGNTVQDVLEAALRQFGGVELPTTVAGRTDAGVHALGQ 60

Query: 61  VAHFD--LVRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           + H D  LVRE   WV     +  NA+L    T+++     V + FHARFSA RR+Y Y 
Sbjct: 61  IIHLDTDLVREAFSWV-----RGTNAFLP--STVAVRWAQAVPEDFHARFSAHRRTYYYA 113

Query: 116 II---TRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRT 171
           ++   TR   L  + G   L P +SLD   M+ AAQ LVG HDF++FR+  CQA SP++T
Sbjct: 114 LVSGPTRSPLLGGKAGYVMLPPGESLDVAAMQEAAQVLVGEHDFSSFRAAECQAKSPVKT 173

Query: 172 IDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECG 231
           +   +V   G  + +R+   +FLH  +R+ +G L  +G G+  +  + + L A+DRK   
Sbjct: 174 LYSAEVRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRRPAAWMAEVLAARDRKAAA 233

Query: 232 PLAPPEGLYFDSVEY 246
           P   P+GLY   V Y
Sbjct: 234 PTFMPDGLYLAEVGY 248


>gi|157374791|ref|YP_001473391.1| tRNA-pseudouridine synthase I [Shewanella sediminis HAW-EB3]
 gi|189030145|sp|A8FTU0|TRUA_SHESH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157317165|gb|ABV36263.1| tRNA-pseudouridine synthase I [Shewanella sediminis HAW-EB3]
          Length = 261

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 94/250 (37%), Positives = 136/250 (54%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G  YFGWQRQ    S+Q  +E+A+  V  E + VH AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYDGRQYFGWQRQAEVDSVQAQLERALSKVANEPIRVHCAGRTDAGVHATGQV 60

Query: 62  AHFDL--VRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+   +R+   W        L   + + D I++  + IVD +FHARFSA  R Y Y I
Sbjct: 61  VHFETNAIRKDSAWT-------LGVNVNLPDDIAVRWVKIVDDEFHARFSATARRYRYMI 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   + +        ++D + M  AAQ  VG HDFT+FR++HCQ+ +P R++   +
Sbjct: 114 YNYDFRPGILRSGVSHYRGNIDADIMHQAAQQFVGEHDFTSFRALHCQSKTPFRSVHEVN 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  I + + A +FLH  +R+ VG+L  +G G      + + L  +DR +  P A P
Sbjct: 174 VTRQGMYICVDIKANAFLHHMVRNIVGTLLEIGLGNQRPEWIPQLLDLKDRSQAAPTAKP 233

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 234 NGLYMVDVTY 243


>gi|170691065|ref|ZP_02882231.1| tRNA pseudouridine synthase A [Burkholderia graminis C4D1M]
 gi|170144314|gb|EDT12476.1| tRNA pseudouridine synthase A [Burkholderia graminis C4D1M]
          Length = 270

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 93/248 (37%), Positives = 134/248 (54%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + I+Y+GS + GWQ Q +G+++Q  +E+A+  F  T    VV  AGRTD+GVH L
Sbjct: 1   MKRIALGIQYDGSAFCGWQSQPHGNTVQDELERALREFAQTPVHTVV--AGRTDTGVHGL 58

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD   E   V   +  N +L    TIS+     + + FHARFSA  R+Y Y +  
Sbjct: 59  GQVVHFDTELERADVSWVRGTNTFLP--KTISVQWAKPMPEAFHARFSAFERTYYYLLYV 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 +   RA  +   LD E MR AA HL+G HDF+ FRS  CQA +PI+ +   D+ 
Sbjct: 117 HPVRSPMLAARAGWVHTPLDIEAMRAAAAHLIGEHDFSAFRSSQCQAKTPIKHLHQIDIE 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ +  R  A +FLH  +R+ +G L  +G  +     + + L ++DR+   P   P+G
Sbjct: 177 QHGDFVHFRFRANAFLHHMVRNLMGCLVYIGKRRRPVEWMAEVLASRDRESAAPTFMPDG 236

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 237 LYLAQVGY 244


>gi|310659467|ref|YP_003937188.1| tRNA pseudouridine synthase a [Clostridium sticklandii DSM 519]
 gi|308826245|emb|CBH22283.1| tRNA pseudouridine synthase A 1 (tRNA-uridine isomerase I 1) (tRNA
           pseudouridylate synthase I 1) [Clostridium sticklandii]
          Length = 249

 Score =  170 bits (430), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    ++IEY+G+ Y GWQRQ N +S+Q  IEKAI+ VT +   ++G+GRTD+ VHAL Q
Sbjct: 1   MRNILILIEYDGTNYNGWQRQPNAASVQEEIEKAIYKVTKKQTDIYGSGRTDAKVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F             ALN  L   D I ILN   V ++FH+R+SA  ++Y YR++   
Sbjct: 61  VANFHTDSAIPTEKFAVALNTNL--PDDIVILNSIEVPEEFHSRYSAKVKTYRYRVLNTP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +E+  A+ + + LD + ++  A+ L+G HDF  F S      + IRTI    +   
Sbjct: 119 VRRPIERNYAYHVREDLDLDIIKTMAKLLIGEHDFKAFSSSGSSVKTTIRTIYDIKITKE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            ++IE       FL+  +R  VG+L  +G  K T  D+++AL   DR   GP APP+GL+
Sbjct: 179 NDIIEFEFTGNGFLYNMVRIIVGTLIELGK-KSTRYDIQRALMTGDRGFAGPTAPPQGLF 237

Query: 241 FDSVEYS 247
              V Y+
Sbjct: 238 LKKVSYN 244


>gi|34498219|ref|NP_902434.1| tRNA pseudouridine synthase A [Chromobacterium violaceum ATCC
           12472]
 gi|42559750|sp|Q7NUD6|TRUA_CHRVO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|34104072|gb|AAQ60432.1| pseudouridylate synthase A [Chromobacterium violaceum ATCC 12472]
          Length = 262

 Score =  170 bits (430), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 92/251 (36%), Positives = 138/251 (54%), Gaps = 13/251 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVVHGAGRTDSGVHALRQ 60
           +R  + IEY+G  + GWQ Q +G+++Q  + +A+  + G   VV H AGRTD+GVHA  Q
Sbjct: 1   MRIALGIEYDGRAFAGWQSQPHGNTVQDRLNRALGQIAGNRDVVTHAAGRTDAGVHAAMQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLK-----ISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD           + LNA+++     +   ++++    V   FHARFSA  RSY Y 
Sbjct: 61  VVHFD-------TDASRPLNAWVRGVNALLPPEVAVVWAREVGDDFHARFSAFSRSYSYF 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           ++T      L  G+     ++LD   MR AA  L+GRHDF++FR+  CQA SP++ +   
Sbjct: 114 LLTHPVRSCLLAGKVGWYHQALDVAAMREAAAGLLGRHDFSSFRASECQAKSPVKDLQRL 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
           D+     L+   + A +FLH  +R+ VG+L  VG G  +  D++  L A+DR    P   
Sbjct: 174 DIIEADGLLRFDLHADAFLHHMVRNIVGALLYVGKGALSPADMQSLLAARDRTSAPPTFM 233

Query: 236 PEGLYFDSVEY 246
           P+GLY   V Y
Sbjct: 234 PDGLYLTGVGY 244


>gi|312882128|ref|ZP_07741878.1| tRNA pseudouridine synthase A [Vibrio caribbenthicus ATCC BAA-2122]
 gi|309370264|gb|EFP97766.1| tRNA pseudouridine synthase A [Vibrio caribbenthicus ATCC BAA-2122]
          Length = 264

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 96/245 (39%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNGS YFGWQRQK   S+Q  +EKA+ +V    V V  AGRTD+GVH   Q+
Sbjct: 1   MKIALGIEYNGSQYFGWQRQKEVKSVQECLEKALSIVANHKVEVQCAGRTDAGVHGTGQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+       V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFETTASRKAVAWTMGANANL--PKDIAVRWAKEVPDEFHARFSATARRYRYLIFNDAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD   M  A Q+L+G +DFT+FR+ HCQ+ SP R + H +V S G
Sbjct: 119 RPGILSSGVSHYHGDLDVTQMHKAGQYLLGENDFTSFRATHCQSKSPWRNLMHLNVTSHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL +VG G+     +   L  +DRK+ G  A  EGLY 
Sbjct: 179 KYIVVDIKANAFVHHMVRNIVGSLLVVGRGEKKPEWIRDLLAIKDRKQAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|260776454|ref|ZP_05885349.1| tRNA pseudouridine synthase A [Vibrio coralliilyticus ATCC BAA-450]
 gi|260607677|gb|EEX33942.1| tRNA pseudouridine synthase A [Vibrio coralliilyticus ATCC BAA-450]
          Length = 264

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 96/245 (39%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ Y+GWQRQK   S+Q  +E+A+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTHYYGWQRQKEVKSVQEKLERALSIVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V     +NA L   + I++     V ++FHARFSA  R Y Y I     
Sbjct: 61  VHFDTSASRKMVAWTMGVNANL--PNDIAVRWAKEVPEEFHARFSATARRYRYIIFNSAF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD E M  A Q+L+G +DFT+FR++HCQ+ SP R I H DV   G
Sbjct: 119 RPGIMSSGVSHYHGELDAEKMHQAGQYLLGENDFTSFRAVHCQSRSPWRNIMHLDVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     ++  L+ +DRK  G  A   GLY 
Sbjct: 179 QYVVIDIKANAFVHHMVRNITGSLICVGRGEQKPEWIKWLLEVKDRKLAGATAKAAGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|17546704|ref|NP_520106.1| tRNA pseudouridine synthase A [Ralstonia solanacearum GMI1000]
 gi|42559848|sp|Q8XXX8|TRUA_RALSO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|17429003|emb|CAD15687.1| probable trna pseudouridine synthase a (trna-uridine isomerasei)
           (trna pseudouridylate synthaseI protein [Ralstonia
           solanacearum GMI1000]
          Length = 274

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 98/252 (38%), Positives = 143/252 (56%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+G+ + GWQ Q +G+++Q  +E A+    G  +    AGRTD+GVHAL Q
Sbjct: 1   MTRIALGIQYDGAAFSGWQSQPHGNTVQDVLEAALREFAGVALPTTVAGRTDAGVHALGQ 60

Query: 61  VAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII- 117
           V H D  LVR+  P    +  NA+L    T+++     + + FHARFSA RR+Y Y +  
Sbjct: 61  VVHLDTELVRD--PFSWVRGTNAFLP--PTVAVRWAQAMPEDFHARFSAHRRTYYYALTY 116

Query: 118 --TRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
             TR   L  + G   L P +SLD   M  AAQ LVG HDF++FR+  CQA SP++T+  
Sbjct: 117 GPTRAPLLEGKAGYVTLPPGQSLDVTAMHEAAQVLVGEHDFSSFRAAECQAKSPVKTMYS 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  + +R+   +FLH  +R+ +G L  +G GK  +  + + L A+DRK   P  
Sbjct: 177 TEVRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGKRPAAWMGEVLAARDRKAAAPTF 236

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V Y
Sbjct: 237 MPDGLYLAEVGY 248


>gi|323493306|ref|ZP_08098429.1| tRNA pseudouridine synthase A [Vibrio brasiliensis LMG 20546]
 gi|323312392|gb|EGA65533.1| tRNA pseudouridine synthase A [Vibrio brasiliensis LMG 20546]
          Length = 264

 Score =  169 bits (429), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 100/246 (40%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ YFGWQRQ+   S+Q  +E A+ +V    + V  AGRTD+GVH   QV
Sbjct: 1   MRIALCIEYNGTQYFGWQRQREVKSVQEKLEHALSIVANHPIEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V      NA L   D I++     V ++FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTASRKMVAWTMGANANL--PDDIAVRWAKEVPEEFHARFSATARRYRYIIFNSAL 118

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD + M  AAQ+L+G +DFT+FR+ HCQ+ SP R + H +V   
Sbjct: 119 RPGILSSGVS-HYHGELDEKKMHQAAQYLLGENDFTSFRATHCQSRSPWRNMMHINVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     +E  L A+DRK  G  A  EGLY
Sbjct: 178 GQYVVIDIKANAFVHHMVRNITGSLICVGRGEQEPQWIEWLLAAKDRKLAGATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVDVDY 243


>gi|167767146|ref|ZP_02439199.1| hypothetical protein CLOSS21_01665 [Clostridium sp. SS2/1]
 gi|167711121|gb|EDS21700.1| hypothetical protein CLOSS21_01665 [Clostridium sp. SS2/1]
 gi|291559527|emb|CBL38327.1| pseudouridylate synthase I [butyrate-producing bacterium SSC/2]
          Length = 248

 Score =  169 bits (429), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 96/244 (39%), Positives = 135/244 (55%), Gaps = 5/244 (2%)

Query: 6   MIIEYNGSGYFGWQR---QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           + IEY+GS Y GWQR     N ++IQG +E  +  +TGE V ++G+GRTD+GVHA  QVA
Sbjct: 7   LTIEYDGSRYQGWQRLGGDSNANTIQGKLESVLSKMTGEDVNINGSGRTDAGVHAYGQVA 66

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           +F          +   L  YL  SD I I+ +S   ++FH+R +A  ++YLYRI      
Sbjct: 67  NFHTDCMMSVSEIKNYLTKYLP-SD-IGIVEVSEASERFHSRLNAKEKTYLYRIAIPGVS 124

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E+   W  P++LD + M  AA  L+G HDF  F SI     S +RTI + ++     
Sbjct: 125 NVFERKYLWYFPETLDIKKMEEAASLLIGTHDFKGFSSIKKTKKSTVRTIYNIEIKKTKK 184

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I+I      FLH  +R   G+L  VG GK    D+ KAL++  R + G  APP+GL+  
Sbjct: 185 EIQISYTGNGFLHNMVRILTGTLVEVGCGKIKPEDITKALESTKRSDAGITAPPQGLFLV 244

Query: 243 SVEY 246
           SVEY
Sbjct: 245 SVEY 248


>gi|237746730|ref|ZP_04577210.1| tRNA pseudouridine synthase A [Oxalobacter formigenes HOxBLS]
 gi|229378081|gb|EEO28172.1| tRNA pseudouridine synthase A [Oxalobacter formigenes HOxBLS]
          Length = 264

 Score =  169 bits (428), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 95/248 (38%), Positives = 135/248 (54%), Gaps = 1/248 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+G+G+ GWQ Q +G ++Q  +E AI   T   +    AGRTD+GVHA  Q
Sbjct: 4   MKRIALGIEYDGTGWRGWQTQPDGMTVQDQLEAAIRQFTRMDMATTCAGRTDAGVHATEQ 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTIS-ILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H D   E +PV   + +N+YL  S  +     +      FHAR SAI R Y Y +   
Sbjct: 64  VVHLDTGLERLPVSWVRGINSYLPSSIAVRWACEVPGGKDGFHARSSAIARRYRYLVYNS 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L K RA  + + LD E MR  A  L+G HDF+ FR+  CQ+ +P++T++   +  
Sbjct: 124 PVRSPLWKNRAGWVFRPLDLEWMREGAGFLLGEHDFSAFRAAECQSITPVKTMNGIGIEK 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GNLI     A +FLH  IR+ VGSL +VG G      +++ L+++DR +  P   P+GL
Sbjct: 184 QGNLIVFTFEANAFLHHMIRNIVGSLIVVGKGNRPPKWMKELLESRDRSQAAPTFMPDGL 243

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 244 YLSRVFYE 251


>gi|212635890|ref|YP_002312415.1| tRNA pseudouridine synthase A [Shewanella piezotolerans WP3]
 gi|226708659|sp|B8CPW5|TRUA_SHEPW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|212557374|gb|ACJ29828.1| tRNA pseudouridine synthase [Shewanella piezotolerans WP3]
          Length = 261

 Score =  169 bits (428), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 135/247 (54%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS Y+GWQRQ +  S+QG +EKA+  V  E + V  AGRTD+GVH   QV
Sbjct: 1   MRVALGIEYDGSRYYGWQRQLDVDSVQGQLEKALSKVANEPITVQCAGRTDTGVHGTGQV 60

Query: 62  AHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HFD   +R+     L   +N    + D I++  + +VD++FHARFSA  R Y Y I   
Sbjct: 61  VHFDTNAIRKETAWTLGVNVN----LPDDIAVRWVKVVDEEFHARFSATARRYRYMIYNH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q    + +        ++D + M  AAQ  VG HDFT+FR++ CQ+ +P R I   +V  
Sbjct: 117 QLRPGILRSGVSHYRGNIDEDKMHQAAQLFVGEHDFTSFRALQCQSKTPFREIHEVNVTR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I + + A +FLH  +R+ VG+L  +G G      +   L  +DR +    A P GL
Sbjct: 177 QGMYICVDIKANAFLHHMVRNIVGTLLEIGKGNQPKEWVNTLLALKDRSKAAATAQPNGL 236

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 237 YLVDVTY 243


>gi|300114593|ref|YP_003761168.1| tRNA pseudouridine synthase A [Nitrosococcus watsonii C-113]
 gi|299540530|gb|ADJ28847.1| tRNA pseudouridine synthase A [Nitrosococcus watsonii C-113]
          Length = 259

 Score =  169 bits (428), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 95/250 (38%), Positives = 136/250 (54%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+GS + GWQ QK   ++Q ++E+A+  V  E V V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGLEYDGSNFSGWQSQKGVRTVQATLERALSTVANEPVTVITAGRTDAGVHAAAQV 60

Query: 62  AHFD-----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD     L   WV             +   ++IL    V++ FHARFSAI R Y Y +
Sbjct: 61  VHFDTTTFRLEHHWV-------FGGNANLPPEVAILWAQPVNEAFHARFSAIARHYRYIV 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           + R+   A+   R     + L    M+ A   LVG HDF++FR+  CQA SP+R + H +
Sbjct: 114 LNRRTRPAIANRRVTWYCQPLSVTKMKEAGAFLVGEHDFSSFRAKACQAKSPVRNVHHLE 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+ I + + A +FLH  +R+  G L  +G G+      E+ LQA+ R   G  A P
Sbjct: 174 VTRQGDWIIMDISANAFLHHMVRNIAGVLMAIGKGEQPPRWAEEVLQARCRAVGGVTARP 233

Query: 237 EGLYFDSVEY 246
           +GLY  SV+Y
Sbjct: 234 DGLYLVSVDY 243


>gi|110802389|ref|YP_699630.1| tRNA pseudouridine synthase A [Clostridium perfringens SM101]
 gi|110682890|gb|ABG86260.1| tRNA pseudouridine synthase A [Clostridium perfringens SM101]
          Length = 244

 Score =  169 bits (428), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 92/241 (38%), Positives = 136/241 (56%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+ YFGWQ+Q  G++IQ  +E+AI  VT E V + G+ RTDSGVHA   VA+F 
Sbjct: 6   LTIEYDGTSYFGWQKQPIGNTIQQKVEEAIKKVTKEEVEILGSSRTDSGVHAKAYVANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                       ALN+  K+   I I+N   V + FHAR+    ++Y Y I+ R+ P AL
Sbjct: 66  TNSNIPGKNFKAALNS--KLPKDIVIMNSEEVAEDFHARYMTTGKTYCYTILNREEPPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
           E+   + + K LD E+M+ A ++ +G+HDF  F+       + +RTI    +   GN I+
Sbjct: 124 ERNYVYHVKKQLDVESMKEACKYFLGKHDFKAFQRPGGTVKTSVRTITDIHIEIEGNKIK 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I V A  FL+  +R  VG+L  VG GK     +++ + + DRK+ G   PP GL  + V 
Sbjct: 184 IYVSADGFLYNMVRLIVGTLLKVGRGKEKPEYIKEVIDSGDRKKAGICVPPTGLCLEKVF 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|313884603|ref|ZP_07818364.1| tRNA pseudouridine synthase A [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620387|gb|EFR31815.1| tRNA pseudouridine synthase A [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 256

 Score =  169 bits (427), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 97/253 (38%), Positives = 138/253 (54%), Gaps = 8/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVH 56
           M RY + +EY+GS Y G+Q Q NG S+Q  +++A+  +        V+   +GRTDSGVH
Sbjct: 1   MPRYAIKVEYDGSNYVGYQVQPNGPSVQAQLDRALLKLAKRPADHPVLTVASGRTDSGVH 60

Query: 57  ALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AL QV HFDL  E  P+ L KALN+ L  +  I ++ +S V   FHAR+ AI ++YLYRI
Sbjct: 61  ALGQVVHFDLDFEIHPLALAKALNSIL--NKDIRVVAVSQVAPDFHARYHAIGKAYLYRI 118

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            T+  P   ++      P   D   M+ A   LVG+HDFT+F S H      +RTI    
Sbjct: 119 DTQAYPDPFKRFYTLHHPYRYDLGKMQRALTDLVGQHDFTSFCSTHSDKEDKVRTIKFAT 178

Query: 177 VNSFGNLIEIR--VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           +       E+R  +    FL+  +R  VG+L  +GDG     + ++ L  +DR + GP A
Sbjct: 179 IEEDLVNQELRFMIAGNGFLYNMVRIIVGTLLQIGDGLKPVDEFKRLLAVKDRNQAGPTA 238

Query: 235 PPEGLYFDSVEYS 247
            P GLY   V+Y 
Sbjct: 239 DPSGLYLYRVDYK 251


>gi|294141648|ref|YP_003557626.1| tRNA pseudouridine synthase A [Shewanella violacea DSS12]
 gi|293328117|dbj|BAJ02848.1| tRNA pseudouridine synthase A [Shewanella violacea DSS12]
          Length = 275

 Score =  169 bits (427), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 133/247 (53%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS Y+GWQRQ    ++Q  +E+A+  V  + + VH AGRTD+GVH   QV
Sbjct: 15  MRVALGIEYDGSKYYGWQRQLEVDTVQAQLERALSKVANQPITVHCAGRTDAGVHGTGQV 74

Query: 62  AHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HF+   +R+     L   +N    + D I++  + +VD  FHARFSA  R Y Y I   
Sbjct: 75  VHFETTAIRKESAWTLGVNVN----LPDDIAVKWVKLVDDDFHARFSATARRYRYLIYNY 130

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                + +         LD   M  AAQH VG HDFT+FR++HCQ+ SP R +   +V  
Sbjct: 131 HLRPGILRSGVSHYRGQLDENKMHQAAQHFVGEHDFTSFRALHCQSKSPFRHVHEVNVTR 190

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A +FLH  +R+ VGSL  +G G      + + L  +DR +  P A P GL
Sbjct: 191 QGMYLCVDIKANAFLHHMVRNIVGSLIEIGQGHQQGDWIVELLALKDRSKAAPTAKPNGL 250

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 251 YMVDVTY 257


>gi|238024257|ref|YP_002908489.1| tRNA pseudouridine synthase A [Burkholderia glumae BGR1]
 gi|237878922|gb|ACR31254.1| Pseudouridylate synthase [Burkholderia glumae BGR1]
          Length = 276

 Score =  169 bits (427), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 85/245 (34%), Positives = 136/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G+++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFHGWQSQPHGNTVQDTLERALKAFARVPLQTVVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L  S  +++     + + FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTELDRTAFSWVRGTNAFLPPS--VAVQWAKPMPEAFHARFAAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +   RA  +   LD E MR AA HL+G HDF++FRS  CQ+ +P++ +   D+   G
Sbjct: 119 RSPMLAARAGWVHTPLDVEAMRAAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDIRPSG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ +  L++ L A++R    P   P+GLY 
Sbjct: 179 SFIHFRFRANAFLHHMVRNLMGCLIAVGRGRYPADWLDEVLAARNRDRAAPTFAPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 AHVGY 243


>gi|299066408|emb|CBJ37593.1| tRNA pseudouridylate synthase I [Ralstonia solanacearum CMR15]
          Length = 274

 Score =  169 bits (427), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 97/252 (38%), Positives = 144/252 (57%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+G+ + GWQ Q +G+++Q  +E A+    G ++    AGRTD+GVHAL Q
Sbjct: 1   MTRIALGIQYDGAAFSGWQSQPHGNTVQDVLEAALREFAGVVLPTTVAGRTDAGVHALGQ 60

Query: 61  VAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII- 117
           V H D  LVR+  P    +  NA+L    T+++     + + FHARFSA RR+Y Y +  
Sbjct: 61  VIHLDTDLVRD--PFSWVRGTNAFLP--PTVAVRWAQAMPEDFHARFSAHRRTYYYALTY 116

Query: 118 --TRQAPLALEKGRAWLIP-KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
             TR   L  + G   L P +SLD   M  AAQ LVG HDF++FR+  CQA SP++T+  
Sbjct: 117 GPTRAPLLEGKAGYVTLPPGQSLDVAAMHEAAQVLVGEHDFSSFRAAECQAKSPVKTMYS 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  + +R+   +FLH  +R+ +G L  +G GK  +  + + L A++RK   P  
Sbjct: 177 AEVRGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGKRPAAWMGEVLAARERKAAAPTF 236

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V Y
Sbjct: 237 MPDGLYLAEVGY 248


>gi|258646072|ref|ZP_05733541.1| tRNA pseudouridine synthase A [Dialister invisus DSM 15470]
 gi|260403447|gb|EEW96994.1| tRNA pseudouridine synthase A [Dialister invisus DSM 15470]
          Length = 246

 Score =  168 bits (426), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + Y  I++Y+G+ Y GWQ+QK    +IQG +EK +  +TGE V V GAGRTD+GVH+L Q
Sbjct: 1   MNYRCIVQYDGTRYEGWQKQKRTEETIQGKLEKTLRKITGEEVQVIGAGRTDAGVHSLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V +F L   W    L  ALN  L   D I++ ++   +++FH+RFS + ++Y YRI T  
Sbjct: 61  VVNFHLKGRWKAEELETALNGDL--PDDIALKHMETAEERFHSRFSTLEKTYRYRIRTST 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                E+   W   KSLD E M+ AA  L+G +DFT+F        S +R I   ++   
Sbjct: 119 EKNVFERRFVWQYGKSLDIEAMKKAAAFLIGTYDFTSFCGNKKMKKSAVRCISGIEMKEI 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              ++I      FL   +R  VG+L  VG+GK  +  +   L+++ R++ G  APP+GL 
Sbjct: 179 KGELQIDFTGDGFLQGMVRILVGTLVEVGEGKRKAESIPAILESKSREKAGFTAPPQGLI 238

Query: 241 FDSVEYS 247
             SV Y 
Sbjct: 239 LVSVRYE 245


>gi|331086292|ref|ZP_08335372.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406058|gb|EGG85581.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 249

 Score =  168 bits (426), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 91/244 (37%), Positives = 132/244 (54%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + I Y+G+ Y GWQ Q NG +++  I KA+  +TGE + V GA RTDSGVHAL  VA
Sbjct: 5   RIKLTIAYDGTNYCGWQVQPNGITVEEVINKALCKLTGEDIAVIGASRTDSGVHALGNVA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            FD      P  +  ALN   ++ D I I+    V   FH R+    ++Y Y II  + P
Sbjct: 65  VFDSATSIPPERIAMALNQ--RLPDDIVIVKSEEVATDFHPRYCDCEKTYEYHIINTRTP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
           +  ++   + +   LD E M+ AA +LVG HDF +F ++  Q    +RT+   +V   G 
Sbjct: 123 IPTKRLTNYFVSYDLDVERMQQAADYLVGEHDFVSFCNVRTQVEDTVRTVTELEVLREGE 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I IR+    FL+  +R  VG+L  VG G +T   +++ L+A+DRK  G  AP  GL   
Sbjct: 183 EITIRISGNGFLYNMVRIIVGTLVRVGRGFYTPEKVKEILEAKDRKAAGVTAPAHGLMLV 242

Query: 243 SVEY 246
            + Y
Sbjct: 243 EIRY 246


>gi|325662523|ref|ZP_08151126.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 4_1_37FAA]
 gi|325471219|gb|EGC74444.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 4_1_37FAA]
          Length = 249

 Score =  168 bits (426), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 91/244 (37%), Positives = 132/244 (54%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + I Y+G+ Y GWQ Q NG +++  I KA+  +TGE + V GA RTDSGVHAL  VA
Sbjct: 5   RIKLTIAYDGTNYCGWQVQPNGITVEEVINKALCKLTGEDIAVIGASRTDSGVHALGNVA 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            FD      P  +  ALN   ++ D I I+    V   FH R+    ++Y Y II  + P
Sbjct: 65  VFDSATSIPPERIAMALNQ--RLPDDIVIVKSEEVAPDFHPRYCDCEKTYEYHIINTRTP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
           +  ++   + +   LD E M+ AA +LVG HDF +F ++  Q    +RT+   +V   G 
Sbjct: 123 IPTKRLTNYFVSYDLDVERMQQAADYLVGEHDFVSFCNVRTQVEDTVRTVTELEVLREGE 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I IR+    FL+  +R  VG+L  VG G +T   +++ L+A+DRK  G  AP  GL   
Sbjct: 183 EITIRISGNGFLYNMVRIIVGTLVRVGRGFYTPEKVKEILEAKDRKAAGVTAPAHGLMLV 242

Query: 243 SVEY 246
            + Y
Sbjct: 243 EIRY 246


>gi|125975420|ref|YP_001039330.1| tRNA pseudouridine synthase A [Clostridium thermocellum ATCC 27405]
 gi|256005284|ref|ZP_05430250.1| tRNA pseudouridine synthase A [Clostridium thermocellum DSM 2360]
 gi|281419381|ref|ZP_06250396.1| tRNA pseudouridine synthase A [Clostridium thermocellum JW20]
 gi|166991160|sp|A3DJK8|TRUA_CLOTH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|125715645|gb|ABN54137.1| tRNA pseudouridine synthase A [Clostridium thermocellum ATCC 27405]
 gi|255990720|gb|EEU00836.1| tRNA pseudouridine synthase A [Clostridium thermocellum DSM 2360]
 gi|281407001|gb|EFB37264.1| tRNA pseudouridine synthase A [Clostridium thermocellum JW20]
 gi|316939545|gb|ADU73579.1| tRNA pseudouridine synthase A [Clostridium thermocellum DSM 1313]
          Length = 244

 Score =  168 bits (426), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 96/242 (39%), Positives = 137/242 (56%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+G+ Y GWQ+QKN  ++Q +IE+AI  +TGE V + GA RTD GVHAL QVA+F 
Sbjct: 6   LIIEYDGTNYHGWQKQKNAKTVQDTIERAIKGLTGEKVDLIGASRTDFGVHALGQVANF- 64

Query: 66  LVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +    +P      ALN  L   D I I     VD  FHAR+ A  + Y Y I   Q P A
Sbjct: 65  ITNSGIPGDRFSYALNRML--PDDIVIKESQEVDMDFHARYKAKGKRYRYLIYNSQFPSA 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L + R + +   LD E+M+ AA + +G HDF+ FRS    A + +RTI    +     ++
Sbjct: 123 LLRHRTYHVSHKLDFESMQRAASYFLGTHDFSAFRSSGSSAKTSVRTITDVSLEREDKIV 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +  +    FL+  +R  VG+L  VG GK  + ++ + ++++ RK  G  AP EGLY   V
Sbjct: 183 KFEIAGDGFLYNMVRIIVGTLMEVGIGKIRADEIPQIIESRKRKRAGRTAPAEGLYLVEV 242

Query: 245 EY 246
            Y
Sbjct: 243 YY 244


>gi|53716174|ref|YP_106286.1| tRNA pseudouridine synthase A [Burkholderia mallei ATCC 23344]
 gi|76817905|ref|YP_335930.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1710b]
 gi|121597592|ref|YP_991241.1| tRNA pseudouridine synthase A [Burkholderia mallei SAVP1]
 gi|126443551|ref|YP_001063441.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 668]
 gi|126456028|ref|YP_001076342.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1106a]
 gi|134278539|ref|ZP_01765253.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 305]
 gi|167724493|ref|ZP_02407729.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei DM98]
 gi|167743453|ref|ZP_02416227.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 14]
 gi|167820639|ref|ZP_02452319.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 91]
 gi|167828999|ref|ZP_02460470.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 9]
 gi|167850474|ref|ZP_02475982.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei B7210]
 gi|167899069|ref|ZP_02486470.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 7894]
 gi|167907414|ref|ZP_02494619.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei NCTC
           13177]
 gi|167915752|ref|ZP_02502843.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 112]
 gi|167923592|ref|ZP_02510683.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei BCC215]
 gi|226195622|ref|ZP_03791209.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei Pakistan
           9]
 gi|237508302|ref|ZP_04521017.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei MSHR346]
 gi|242312379|ref|ZP_04811396.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1106b]
 gi|254186230|ref|ZP_04892748.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei Pasteur
           52237]
 gi|254194496|ref|ZP_04900928.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei S13]
 gi|254265540|ref|ZP_04956405.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1710a]
 gi|254301278|ref|ZP_04968722.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 406e]
 gi|254359267|ref|ZP_04975539.1| tRNA pseudouridine synthase A [Burkholderia mallei 2002721280]
 gi|62901257|sp|Q62AJ2|TRUA_BURMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123597008|sp|Q3JKH3|TRUA_BURP1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228685|sp|A1UZ38|TRUA_BURMS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228686|sp|A3P7N2|TRUA_BURP0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228687|sp|A3NM70|TRUA_BURP6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|52422144|gb|AAU45714.1| tRNA pseudouridine synthase A [Burkholderia mallei ATCC 23344]
 gi|76582378|gb|ABA51852.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1710b]
 gi|121225390|gb|ABM48921.1| tRNA pseudouridine synthase A [Burkholderia mallei SAVP1]
 gi|126223042|gb|ABN86547.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 668]
 gi|126229796|gb|ABN93209.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1106a]
 gi|134250323|gb|EBA50403.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 305]
 gi|148028454|gb|EDK86414.1| tRNA pseudouridine synthase A [Burkholderia mallei 2002721280]
 gi|157811288|gb|EDO88458.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 406e]
 gi|157933916|gb|EDO89586.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei Pasteur
           52237]
 gi|169651247|gb|EDS83940.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei S13]
 gi|225932107|gb|EEH28107.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei Pakistan
           9]
 gi|235000507|gb|EEP49931.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei MSHR346]
 gi|242135618|gb|EES22021.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1106b]
 gi|254216542|gb|EET05927.1| tRNA pseudouridine synthase A [Burkholderia pseudomallei 1710a]
          Length = 270

 Score =  168 bits (426), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+++       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQSQPHGKTVQDALERSLAEFAQTSLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTDLDRADFSWVRGTNAFLP--PTVAVQWAKPMPDTFHARFAAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GRA  +   LD + MR AA HLVG HDF+ FRS  CQA SP++ +    +   G
Sbjct: 119 RSPMLAGRAGWVHTPLDVDAMREAAAHLVGEHDFSAFRSSECQAKSPVKHLYQIGIRPDG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ S+ L + L+++DR    P   PEGLY 
Sbjct: 179 DFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPSSWLAEVLESRDRDCAAPTFMPEGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 AHVGY 243


>gi|323529192|ref|YP_004231344.1| tRNA pseudouridine synthase A [Burkholderia sp. CCGE1001]
 gi|323386194|gb|ADX58284.1| tRNA pseudouridine synthase A [Burkholderia sp. CCGE1001]
          Length = 270

 Score =  168 bits (426), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + ++Y+GS + GWQ Q +G+++Q  +E+A+       V    AGRTD+GVH L Q
Sbjct: 1   MKRIALGVQYDGSAFCGWQSQPHGNTVQDELERALREFAQTPVQTVVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E   +   +  N++L    T+S+     + + FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELERADISWVRGTNSFLP--KTVSVQWAKPMPEAFHARFSAFERTYYYVLYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   RA  +  SLD + MR AA HL+G HDF+ FRS  CQA +P++ +   D+   
Sbjct: 119 VRSPMLAARAGWVHASLDIDAMREAAVHLIGEHDFSAFRSSQCQAKTPVKHLYQIDIQQQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +  R  A +FLH  +R+ +G L  +G G+     + + L+ +DR+   P   P+GLY
Sbjct: 179 GDFVHFRFRANAFLHHMVRNVMGCLVYIGKGRRPVQWMAEVLEGRDREWAAPTFMPDGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAQVGY 244


>gi|121998585|ref|YP_001003372.1| tRNA pseudouridine synthase A [Halorhodospira halophila SL1]
 gi|121589990|gb|ABM62570.1| tRNA pseudouridine synthase A [Halorhodospira halophila SL1]
          Length = 266

 Score =  168 bits (426), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 95/249 (38%), Positives = 132/249 (53%), Gaps = 12/249 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  +++EY+G+G+ GWQRQ +  S+Q ++E A+  +    V V  AGRTD+GVHA  QV 
Sbjct: 9   RIALVLEYDGTGFSGWQRQDDAPSVQEALEGAVSRIANHPVAVVCAGRTDAGVHAAAQVV 68

Query: 63  HFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           HFD      +  WV       L    ++ +T+S+ +   VD  FHAR+ A RR Y Y  +
Sbjct: 69  HFDTTASRPLHAWV-------LGTNAQLPETVSVRSAHAVDADFHARYQAQRRGYRYVFL 121

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
            R+A  AL + R       LD   M  AAQ LVG HDF+ FR+  CQA   +R +   DV
Sbjct: 122 CRRARPALLRHRVAWTHHELDEGRMHRAAQALVGEHDFSAFRAAACQAPHAVREVYRLDV 181

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
           +  G L+ I + A +F+H  +R+  G+L  VG G+         L A DR   G  AP  
Sbjct: 182 HRHGELLFIDIEANAFVHHMVRNIAGTLMAVGTGEQPEHWPAGLLAAGDRTRSGMTAPAA 241

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 242 GLYLTRVVY 250


>gi|99034196|ref|ZP_01314273.1| hypothetical protein Wendoof_01000930 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 166

 Score =  168 bits (426), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 85/167 (50%), Positives = 115/167 (68%), Gaps = 2/167 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +RY + +EYNGS + GWQ+Q++  +SIQ  IE AIF  +GE V ++  GRTD+GVHAL Q
Sbjct: 1   MRYKITVEYNGSNFSGWQKQQHSANSIQEKIENAIFNFSGEKVTLYCGGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD+ +E+    +  A+N +LK S  I +LN  +VD  FHARFSA +R Y YRI+ R 
Sbjct: 61  VAHFDMEKEFELYRIRNAINYHLK-SIPIVVLNAEVVDDAFHARFSAKKRYYEYRIVNRY 119

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASS 167
           AP ALE G  W +   LD   MR AA+HL+G+HD ++FRS  CQA++
Sbjct: 120 APAALETGYVWQVFSPLDVNIMREAAKHLLGKHDLSSFRSKDCQAAN 166


>gi|114775677|ref|ZP_01451245.1| tRNA pseudouridine synthase A [Mariprofundus ferrooxydans PV-1]
 gi|114553788|gb|EAU56169.1| tRNA pseudouridine synthase A [Mariprofundus ferrooxydans PV-1]
          Length = 267

 Score =  168 bits (426), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 92/247 (37%), Positives = 138/247 (55%), Gaps = 5/247 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + +E++G  + GWQ+Q+N +S+Q  ++ A+  V GE + V  AGRTD+GVHA   + 
Sbjct: 11  RIALALEFDGRPFHGWQQQENATSVQACLQDALQAVEGEPLTVVAAGRTDAGVHAEALLV 70

Query: 63  HFDL-VREW--VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           H D+    W   P       N++L   D I ++ +  V   FHARF+   RSY Y+I  R
Sbjct: 71  HADVSAARWQRSPRAYLHGCNSHLP--DEIRVVGVRAVAADFHARFACRGRSYRYQIWNR 128

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL++ R W +P+SL+ E M+ AA H +GRHDF+  R+  CQA+   + I   ++  
Sbjct: 129 NTASALQRWRHWWMPRSLNIEAMQGAAVHCLGRHDFSALRAAGCQAAHAEKHIRSLEIVQ 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ I I V A +FL+  +R+ VG+L  VG GK +  D    L ++DR+     AP  GL
Sbjct: 189 HGHCIHIHVSADAFLYHMVRNLVGNLVEVGAGKRSPDDFAALLASRDRQLGAATAPAHGL 248

Query: 240 YFDSVEY 246
           YF    Y
Sbjct: 249 YFTDAWY 255


>gi|254228474|ref|ZP_04921900.1| tRNA pseudouridine synthase A [Vibrio sp. Ex25]
 gi|262393647|ref|YP_003285501.1| tRNA pseudouridine synthase A [Vibrio sp. Ex25]
 gi|151939062|gb|EDN57894.1| tRNA pseudouridine synthase A [Vibrio sp. Ex25]
 gi|262337241|gb|ACY51036.1| tRNA pseudouridine synthase A [Vibrio sp. Ex25]
          Length = 264

 Score =  168 bits (425), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 135/247 (54%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ YFGWQRQ+   S+Q  +EKA+ ++    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTNYFGWQRQREVKSVQEELEKALSVIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HFD  + R+    ++   + A   +   I++     V   FHARFSA  R Y Y I   
Sbjct: 61  VHFDTNVTRK----MVAWTMGANANMPSDIAVRWAKEVPDDFHARFSATARRYRYIIFNH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                +           LD + M  A Q+L+G +DFT+FR+ HCQ+ SP R + H +V  
Sbjct: 117 ALRPGILNSGVSHYHGELDEKKMHEAGQYLLGENDFTSFRAAHCQSRSPFRNLMHLNVTR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN + I + A +F+H  +R+  GSL  VG G+ +   ++  L+A+DRK  G  A  EGL
Sbjct: 177 HGNYVVIDIKANAFVHHMVRNITGSLIKVGRGEESPEWIKWLLEAKDRKLAGATAKAEGL 236

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 237 YLVDVDY 243


>gi|158520483|ref|YP_001528353.1| tRNA pseudouridine synthase A [Desulfococcus oleovorans Hxd3]
 gi|158509309|gb|ABW66276.1| tRNA pseudouridine synthase A [Desulfococcus oleovorans Hxd3]
          Length = 252

 Score =  168 bits (425), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 100/243 (41%), Positives = 135/243 (55%), Gaps = 5/243 (2%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIEY+G+ + GWQ QK+  ++QG I  A+  +TG+ V V G+GRTD+GVHA+ QVA F 
Sbjct: 7   LIIEYDGACFHGWQIQKDLRTVQGEITGALASITGQAVSVIGSGRTDAGVHAMAQVASFI 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P  L KALN  L  +  I I +   V   FHAR+SA  ++Y YRI+ R  P AL
Sbjct: 67  CDTRLEPGTLQKALNGIL--AKDIVIHDCREVSLNFHARYSAKSKTYRYRILNRNLPAAL 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR--TIDHFDVNSFGNL 183
            +G AW I K LD   M  A  H++GRHDF++F       +S +R  T   F++   G L
Sbjct: 125 YRGYAWHIKKPLDLGAMTAALPHILGRHDFSSFEGTGSPKASSVRHVTAATFNMAEDGYL 184

Query: 184 IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDS 243
               + A  FL   +R+ VG+L  VG GK T   +   L A+DR   G  AP  GL+   
Sbjct: 185 -AFEITADGFLKHMVRNIVGTLVEVGLGKKTPEAVADILAAKDRSRAGATAPGHGLFLVR 243

Query: 244 VEY 246
           V Y
Sbjct: 244 VNY 246


>gi|300691102|ref|YP_003752097.1| tRNA pseudouridylate synthase I [Ralstonia solanacearum PSI07]
 gi|299078162|emb|CBJ50805.1| tRNA pseudouridylate synthase I [Ralstonia solanacearum PSI07]
          Length = 274

 Score =  167 bits (424), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 97/252 (38%), Positives = 145/252 (57%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+G+ + GWQ Q +G+++Q  +E A+    G  +    AGRTD+GVHAL Q
Sbjct: 1   MTRIALGIQYDGAAFSGWQSQPHGNTVQDVLEAALRQFAGVELPTIVAGRTDAGVHALGQ 60

Query: 61  VAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V H D  LVR+  P    +  NA+L    T+++     V + FHARFSA RR+Y Y +++
Sbjct: 61  VVHLDTDLVRD--PFSWVRGTNAFLP--PTVAVRWAQEVPEDFHARFSAHRRTYYYALVS 116

Query: 119 --RQAPLALEKGRAWLIP--KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
              +APL   K    ++P  +SLD   M+ AAQ LVG HDF++FR+  CQA SP++T+  
Sbjct: 117 GPTRAPLLGGKAGYVMLPPGESLDVAAMQEAAQVLVGEHDFSSFRAAECQAKSPVKTMYS 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +    G  + +R+   +FLH  +R+ +G L  +G GK     + + L A+DRK   P  
Sbjct: 177 AEARGQGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGKRPVAWMGEVLAARDRKVAAPTF 236

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V Y
Sbjct: 237 MPDGLYLAEVGY 248


>gi|91223605|ref|ZP_01258870.1| tRNA pseudouridine synthase A [Vibrio alginolyticus 12G01]
 gi|269966027|ref|ZP_06180119.1| tRNA pseudouridine synthase A [Vibrio alginolyticus 40B]
 gi|91191691|gb|EAS77955.1| tRNA pseudouridine synthase A [Vibrio alginolyticus 12G01]
 gi|269829423|gb|EEZ83665.1| tRNA pseudouridine synthase A [Vibrio alginolyticus 40B]
          Length = 264

 Score =  167 bits (424), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 134/247 (54%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ YFGWQRQ+   S+Q  +EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTNYFGWQRQREVKSVQEELEKALSVVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HFD  + R+    ++   + A   +   I++     V   FHARFSA  R Y Y I   
Sbjct: 61  VHFDTNVTRK----MVAWTMGANANMPSDIAVRWAKEVSDDFHARFSATARRYRYIIFNH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                +           LD + M  A Q L+G +DFT+FR+ HCQ+ SP R + H +V  
Sbjct: 117 ALRPGILNSGVSHYHGELDEKKMHEAGQFLLGENDFTSFRAAHCQSRSPFRNLMHLNVTR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN + I + A +F+H  +R+  GSL  VG G+ +   ++  L+A+DRK  G  A  EGL
Sbjct: 177 HGNYVVIDIKANAFVHHMVRNITGSLIKVGRGEESPEWIKWLLEAKDRKLAGATAKAEGL 236

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 237 YLVDVDY 243


>gi|167577247|ref|ZP_02370121.1| tRNA pseudouridine synthase A [Burkholderia thailandensis TXDOH]
          Length = 270

 Score =  167 bits (424), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQSQPHGKTVQDALERALAEFAQTSLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTDLDRADFSWVRGTNAFLP--STVAVQWAKPMPDTFHARFAAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +   RA  +   LD + MR AA+HLVG HDF+ FRS  CQA SP++ +    +   G
Sbjct: 119 RSPMLAARAGWVHTPLDVDAMREAAEHLVGEHDFSAFRSSECQAKSPVKHLYQIGIRPDG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ ++ L + L+++DR    P   PEGLY 
Sbjct: 179 DFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPASWLAEVLESRDRDCAAPTFMPEGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 AHVGY 243


>gi|307726601|ref|YP_003909814.1| tRNA pseudouridine synthase A [Burkholderia sp. CCGE1003]
 gi|307587126|gb|ADN60523.1| tRNA pseudouridine synthase A [Burkholderia sp. CCGE1003]
          Length = 270

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 89/248 (35%), Positives = 136/248 (54%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + ++Y+G+ + GWQ Q +G+++Q  +E+A+  F  T    VV  AGRTD+GVH L
Sbjct: 1   MKRIALGVQYDGTAFCGWQSQPHGNTVQDELERALREFAQTPVHTVV--AGRTDTGVHGL 58

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD   E   V   +  N++L    TIS+     + + FHARFSA  R+Y Y +  
Sbjct: 59  GQVVHFDTELERADVSWVRGTNSFLP--KTISVQWAKPMPEAFHARFSAFERTYYYVLYV 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 +  GRA  +  +LD + M  AA HL+G HDF+ FRS  CQ+ +P++ +   D+ 
Sbjct: 117 HPVRSPMLAGRAGWVHAALDIDAMHAAAAHLIGEHDFSAFRSSQCQSKTPVKHLYQIDIQ 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ +  R  A +FLH  +R+ +G L  +G G+     + + L  +DR+   P   P+G
Sbjct: 177 QHGDFVHFRFRANAFLHHMVRNVMGCLVYIGKGRRPVQWMAEVLAGRDREWAAPTFMPDG 236

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 237 LYLAQVGY 244


>gi|154505512|ref|ZP_02042250.1| hypothetical protein RUMGNA_03049 [Ruminococcus gnavus ATCC 29149]
 gi|153794170|gb|EDN76590.1| hypothetical protein RUMGNA_03049 [Ruminococcus gnavus ATCC 29149]
          Length = 246

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 137/247 (55%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +++  + +A+  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRLKLTVAYDGTNYCGWQIQPNGITVEEVLNRALRKLTGEEITVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P  +  ALN   ++ D I ++    V   +H R+   +++Y Y I+  +
Sbjct: 61  VAVFDSETSIPPERISYALNQ--RLPDDIVVIRSEEVSADWHPRYCNSKKTYEYHILNAK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +   + +   LD E M+ AAQ+LVG HDF +F ++       +RTI   D+   
Sbjct: 119 IPDPTRRLTRYFVSFDLDIEKMKKAAQYLVGTHDFVSFCNVRTDVEDTVRTIYSLDILPV 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I IR+    FL+  +R  VG+L  VG G +T   +++ L+A++RK  G  APP+GL+
Sbjct: 179 GDEITIRIQGNGFLYNMVRIIVGTLVRVGRGFYTPEQVQEILEAKNRKAAGVTAPPQGLF 238

Query: 241 FDSVEYS 247
              +EY 
Sbjct: 239 LVGIEYE 245


>gi|21672480|ref|NP_660547.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|25091459|sp|Q8K9U4|TRUA_BUCAP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|21623097|gb|AAM67758.1| tRNA pseudouridine synthase A [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
          Length = 263

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 96/244 (39%), Positives = 137/244 (56%), Gaps = 3/244 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           ++ + +EY+GS Y GWQ QK  S+IQ  IEKA+  +    V V  AGRTDSGVH++ QV 
Sbjct: 8   KFALGVEYDGSYYHGWQSQKGLSTIQSEIEKALSKIANHQVNVICAGRTDSGVHSIGQVI 67

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF  +           +N+YL  S  IS+  +  V + F+AR+SAI RSY Y I   +  
Sbjct: 68  HFTSISFRSDFSWIVGVNSYL--SKNISVKWIKEVSENFNARYSAISRSYRYIIYNHKCR 125

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+ + R+  + K L+ + M   AQ L+G HDF++FRS  CQ+ SP RTI   ++    N
Sbjct: 126 SAIFRNRSNHVYKELNVDKMYFEAQSLLGEHDFSSFRSSGCQSRSPFRTITDLNIRRLKN 185

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           L+ I + A SFL+  +R+ VGSL  + D       ++K L  +DR   GP     GLY  
Sbjct: 186 LVIIDITANSFLYHMVRNIVGSLIQINDNT-KKNYIKKILDKKDRNYAGPTVSARGLYLF 244

Query: 243 SVEY 246
            V+Y
Sbjct: 245 FVKY 248


>gi|254786497|ref|YP_003073926.1| tRNA pseudouridine synthase A [Teredinibacter turnerae T7901]
 gi|237685680|gb|ACR12944.1| tRNA pseudouridine synthase A [Teredinibacter turnerae T7901]
          Length = 286

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 99/252 (39%), Positives = 141/252 (55%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + +EY G+ + G+Q+Q +   ++Q  +E+AI  V  E V +  AGRTD+GV A  
Sbjct: 22  MQRVALGVEYLGASFRGFQKQASTPDTVQARLERAISAVAAEEVTLVCAGRTDAGVSASG 81

Query: 60  QVAHFDLVREWVPVILCKALNAYLK-----ISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD        +  + L A+L+     + D + +     V   FHARFSA+ R+Y Y
Sbjct: 82  QVIHFD-------TLSSRPLKAWLQGVNTHLPDAVRVTWAMPVSFHFHARFSALSRTYHY 134

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            I T     AL   +      SLD E M++AA+ L+G HDF++FR+  CQA SP+R I  
Sbjct: 135 WIQTEPVRSALFSQQLTWTGHSLDVERMQLAAESLLGEHDFSSFRAAQCQAHSPVREIQA 194

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
                +GNLI  RV A +FLH  +R+ +GSL LVG G  + + +E+ L A+DR    P A
Sbjct: 195 VSFERYGNLILFRVRANAFLHHMVRNLIGSLMLVGRGLQSPSWIEQLLAARDRTLAAPTA 254

Query: 235 PPEGLYFDSVEY 246
            P GL   +VEY
Sbjct: 255 APWGLSLVAVEY 266


>gi|302876500|ref|YP_003845133.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|307687172|ref|ZP_07629618.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
 gi|302579357|gb|ADL53369.1| tRNA pseudouridine synthase A [Clostridium cellulovorans 743B]
          Length = 244

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 90/242 (37%), Positives = 141/242 (58%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I+EY+G+ Y GWQ+QKN  ++QG+IEKAI  +T E V + G  RTDSGVHA    A+F 
Sbjct: 6   LILEYDGTKYSGWQKQKNSVTVQGTIEKAIEAITKESVELIGCSRTDSGVHAKGYTANF- 64

Query: 66  LVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                +P+     A+NA  K+ + I IL+   V + FH+RF+ I ++Y Y ++ R +  A
Sbjct: 65  FTNSKIPIERFYIAINA--KLPEDIVILSSEEVPEDFHSRFNCIGKTYCYSVLNRVSYPA 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           + +   + +P+ L  + M+ AA+  VG +DF  FR++  + +S +RTI   +V   G++I
Sbjct: 123 MYRNYLYHVPRKLSIDEMKKAAESFVGTYDFNAFRNLGTEVASTVRTIHRIEVEEHGDII 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I V    FL+  +R   G+L  VG G+  S  ++  L+++DR   G  AP  GL  D V
Sbjct: 183 NILVTGDGFLYNMVRIIAGTLVEVGLGQKRSDQIKVILESKDRNRAGKTAPARGLSLDKV 242

Query: 245 EY 246
            Y
Sbjct: 243 YY 244


>gi|83718190|ref|YP_438876.1| tRNA pseudouridine synthase A [Burkholderia thailandensis E264]
 gi|167621345|ref|ZP_02389976.1| tRNA pseudouridine synthase A [Burkholderia thailandensis Bt4]
 gi|257141962|ref|ZP_05590224.1| tRNA pseudouridine synthase A [Burkholderia thailandensis E264]
 gi|123753984|sp|Q2T7H3|TRUA_BURTA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|83652015|gb|ABC36079.1| tRNA pseudouridine synthase A [Burkholderia thailandensis E264]
          Length = 270

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E+A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQSQPHGKTVQDALERALAEFAQTSLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    T+++     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTDLDRADFSWVRGTNAFLP--STVAVQWAKPMPDTFHARFAAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +   RA  +   LD + MR AA+HLVG HDF+ FRS  CQA SP++ +    +   G
Sbjct: 119 RSPMLAARAGWVHTPLDVDAMREAAEHLVGEHDFSAFRSSECQAKSPVKHLYQIGIRPDG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ ++ L + L+++DR    P   PEGLY 
Sbjct: 179 DFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPASWLAEVLESRDRGCAAPTFMPEGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 AHVGY 243


>gi|241663409|ref|YP_002981769.1| tRNA pseudouridine synthase A [Ralstonia pickettii 12D]
 gi|309783472|ref|ZP_07678175.1| tRNA pseudouridine synthase A [Ralstonia sp. 5_7_47FAA]
 gi|240865436|gb|ACS63097.1| tRNA pseudouridine synthase A [Ralstonia pickettii 12D]
 gi|308917758|gb|EFP63452.1| tRNA pseudouridine synthase A [Ralstonia sp. 5_7_47FAA]
          Length = 274

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 96/252 (38%), Positives = 143/252 (56%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+G+ + GWQ Q +G+++Q  +E A+    G  +    AGRTD+GVHAL Q
Sbjct: 1   MTRIALGIQYDGAAFSGWQSQPHGNTVQDVLESALRQFAGVALPTTVAGRTDAGVHALGQ 60

Query: 61  VAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII- 117
           V H D  LVRE  P    +  NA+L    T+++     + + FHARFSA RR+Y Y +  
Sbjct: 61  VVHLDTDLVRE--PFSWVRGTNAFLP--PTVAVRWAQEMPEGFHARFSAHRRTYYYALTF 116

Query: 118 -TRQAPLALEKGRAWLIP--KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
              +APL  +K    ++P  +SLD E M  AAQ LVG HDF++FR+  CQA SP++T+  
Sbjct: 117 GPTRAPLLEDKAGYVMLPPGQSLDVEAMNEAAQVLVGEHDFSSFRAAECQAKSPVKTMYS 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  + +R+   +FLH  +R+ +G L  +G G+   + +   L A+ R    P  
Sbjct: 177 VEVRGEGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRQPVSWMGDVLAARSRVAAAPTF 236

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V Y
Sbjct: 237 MPDGLYLAEVGY 248


>gi|332284539|ref|YP_004416450.1| tRNA pseudouridine synthase A [Pusillimonas sp. T7-7]
 gi|330428492|gb|AEC19826.1| tRNA pseudouridine synthase A [Pusillimonas sp. T7-7]
          Length = 267

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 92/239 (38%), Positives = 129/239 (53%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           + Y+GS + GWQ Q  G ++Q ++E A+       V    AGRTD+GVHAL Q+ H D  
Sbjct: 5   LAYDGSSWQGWQTQPGGLTVQDTLESALAEFLNHPVGTICAGRTDTGVHALEQIVHLDTQ 64

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
               P    + LNA L  S  I++     V   FHARFSA+ RSY+Y +   +    L  
Sbjct: 65  AARRPESWVRGLNALLPAS--IAVQWAKPVSDSFHARFSALSRSYVYIVRNTRVRSPLMH 122

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
           GR   +  SL  + MR AA+ LVG HDF++FRS  CQA+SP+RT+    V   G+    R
Sbjct: 123 GRVGWVYHSLQLDPMRDAARRLVGEHDFSSFRSSQCQAASPVRTLQEASVEQHGDFYLFR 182

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
             A +FLH  IR+ +G++  +G GK     +++ L  +DR+   P   P GLY   V Y
Sbjct: 183 FQANAFLHHMIRNLMGAILYIGQGKQEPGWIDELLAQRDRRRAAPTFSPAGLYLSGVRY 241


>gi|229074353|ref|ZP_04207391.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock4-18]
 gi|228708795|gb|EEL60930.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock4-18]
          Length = 245

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MHNYKLTIQYDGARYKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFKSDEKLVEHKVKKYLNQYL--PNDISITNVEEVPDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ E+M+ AA+HLVG HDFT F +   +  S +R +   +V+ 
Sbjct: 119 EHTNPFMRKHSMHVNKKLNVESMKKAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLEVSE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y +SVE+
Sbjct: 239 YLESVEF 245


>gi|303257106|ref|ZP_07343120.1| tRNA pseudouridine synthase A [Burkholderiales bacterium 1_1_47]
 gi|302860597|gb|EFL83674.1| tRNA pseudouridine synthase A [Burkholderiales bacterium 1_1_47]
          Length = 259

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 135/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G  + GWQ Q +G ++Q  +E A+   TGE V    AGRTD+ VHA  QV
Sbjct: 1   MRVALGLEYDGRSFEGWQTQPSGQTVQDYLEAAVVQFTGEKVKAVCAGRTDANVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D   +   +   + LN+YL      ++    +V  +FHARFSA  R+Y Y I+    
Sbjct: 61  IHLDTGADRKEISWVRGLNSYLPTE--CAVRWAKVVPDEFHARFSACSRTYEYWIVNEPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GR   + + L+ +NM  A Q LVG HDF++FR+  CQ+ +P++ I++  V   G
Sbjct: 119 RSPILSGRTGWVFRPLNEKNMEAAGQFLVGEHDFSSFRAAGCQSKTPVKNIEYLHVIRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I+IRV A +FL+  +R+ VG L  VG G  +   + + L+A+ R+   P   P GLY 
Sbjct: 179 RFIKIRVKANAFLYHMVRNIVGCLVYVGTGARSVDWMGEVLEAKSRQAAAPTFYPTGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 TGVGY 243


>gi|163750187|ref|ZP_02157429.1| tRNA pseudouridine synthase A [Shewanella benthica KT99]
 gi|161330043|gb|EDQ01027.1| tRNA pseudouridine synthase A [Shewanella benthica KT99]
          Length = 261

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 133/247 (53%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS Y+GWQRQ    ++Q  +E+A+  V  + + VH AGRTDSGVH   QV
Sbjct: 1   MRVALGIEYDGSKYYGWQRQLEVDTVQAQLERALSKVANQPISVHCAGRTDSGVHGTGQV 60

Query: 62  AHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HF+   +R+     L   +N    + D I++  + +VD  FHARFSA  R Y Y I   
Sbjct: 61  VHFETTAIRKESAWTLGVNVN----LPDDIAVKWVKLVDDDFHARFSATARRYRYIIYNY 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                + +         LD + M  AAQH VG HDFT+FR++HCQ+ +P R +   +V  
Sbjct: 117 HLRPGILRSGVSHYRGQLDEDKMHHAAQHFVGEHDFTSFRALHCQSKTPFRHVHEVNVTR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A +FLH  +R+ VGSL  +G G      +   L  +DR +  P A P GL
Sbjct: 177 QGMYLCVDIKANAFLHHMVRNIVGSLIEIGLGHQNEDWIVSLLALKDRSKAAPTAKPNGL 236

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 237 YMVDVTY 243


>gi|195940683|ref|ZP_03086065.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4024]
 gi|295098046|emb|CBK87136.1| pseudouridylate synthase I [Enterobacter cloacae subsp. cloacae
           NCTC 9394]
          Length = 270

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 97/245 (39%), Positives = 135/245 (55%), Gaps = 4/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  RIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPISVFCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQA 121
           HFD             +NA L     I++  +  V   FHARFSA  R Y Y I   R  
Sbjct: 71  HFDTTAVRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYVIYNQRLR 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P  L +G      + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +G
Sbjct: 129 PAVLSQGVTHFY-EPLDAERMQRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVSRYG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY 
Sbjct: 188 AYVVVDIKANAFVHHMVRNIVGSLMEVGAGHQPESWIAELLAAKDRTLAAATAKAEGLYL 247

Query: 242 DSVEY 246
            SV+Y
Sbjct: 248 VSVDY 252


>gi|238022472|ref|ZP_04602898.1| hypothetical protein GCWU000324_02380 [Kingella oralis ATCC 51147]
 gi|237867086|gb|EEP68128.1| hypothetical protein GCWU000324_02380 [Kingella oralis ATCC 51147]
          Length = 260

 Score =  167 bits (422), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 96/252 (38%), Positives = 137/252 (54%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + + YNGS +FG+Q+Q  G  +IQ ++E A+  + GE V +  AGRTD+GVHA  
Sbjct: 1   MTRYALTLSYNGSAFFGFQKQAAGIPTIQTALEHALAQIAGEPVAITAAGRTDTGVHATA 60

Query: 60  QVAHFD-----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD      +  WV     + +NA+L   D I++L+   V   FHARF A  R Y Y
Sbjct: 61  QVVHFDSHATRPLTAWV-----RGVNAHLP--DGIAVLHAQAVAPDFHARFDACGRHYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            + +      L  GRA      LD   M+ AA  L+G HDF++FR+  CQA SP++T+  
Sbjct: 114 LLQSAPVRSPLLVGRAGWTHYPLDMAAMQKAAALLLGEHDFSSFRAAECQAKSPVKTVYA 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
              +   + I+I   A +FLH  +R+ VG+L  VG G+    +  +   AQ R    P  
Sbjct: 174 IAFSGCPSFIKIDFHANAFLHHMVRNIVGALVYVGCGRLAVGEFAEMFAAQSRLTAPPTF 233

Query: 235 PPEGLYFDSVEY 246
             +GLYF  V+Y
Sbjct: 234 MADGLYFTGVDY 245


>gi|330820903|ref|YP_004349765.1| Pseudouridylate synthase [Burkholderia gladioli BSR3]
 gi|327372898|gb|AEA64253.1| Pseudouridylate synthase [Burkholderia gladioli BSR3]
          Length = 277

 Score =  167 bits (422), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 89/248 (35%), Positives = 138/248 (55%), Gaps = 8/248 (3%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIE---KAIFLVTGEIVVVHGAGRTDSGVHAL 58
           +R  + I+Y+G+ + GWQ Q +G ++Q  +E   KA  LV  + VV   AGRTD+GVH L
Sbjct: 1   MRIALGIQYDGAAFCGWQSQPHGKTVQDELERALKAFALVPLQTVV---AGRTDTGVHGL 57

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD   +       +  NA+L    T+++     +   FHARF+A  R+Y Y +  
Sbjct: 58  GQVVHFDTDLDRSDFSWVRGTNAFLP--STVAVQWAKPMPDSFHARFAAFERTYYYALYV 115

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 +   RA  +   LD E MR AA+HL+G HDF++FRS  CQ+ +P++ +   D+ 
Sbjct: 116 HPVRSPMLASRAGWVHTPLDIEAMREAARHLIGEHDFSSFRSSECQSKTPVKHLYQIDIR 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           + G+ I  R  A +FLH  +R+ +G L  VG G++ +  + + L A++R+   P   P+G
Sbjct: 176 ASGSFIHFRFRANAFLHHMVRNLMGCLIAVGRGRYPADWMAEVLAARNRERAAPTFAPDG 235

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 236 LYLAHVGY 243


>gi|228995804|ref|ZP_04155464.1| tRNA pseudouridine synthase A 2 [Bacillus mycoides Rock3-17]
 gi|229003424|ref|ZP_04161244.1| tRNA pseudouridine synthase A 2 [Bacillus mycoides Rock1-4]
 gi|228757802|gb|EEM07027.1| tRNA pseudouridine synthase A 2 [Bacillus mycoides Rock1-4]
 gi|228763965|gb|EEM12852.1| tRNA pseudouridine synthase A 2 [Bacillus mycoides Rock3-17]
          Length = 245

 Score =  167 bits (422), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 141/247 (57%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G  Y GWQR   N ++IQG IE  +  +TG  + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGGRYKGWQRLGNNDNTIQGKIESVLSEMTGREIEIIGCSRTDAGVHALH 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F +      + + K LN YL   + ISI ++ +V ++FHAR+++  ++YLY+I   
Sbjct: 61  QVANFKIDENLPELKVKKYLNQYL--PNDISITDVELVSERFHARYNSKSKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ENM+ AAQ+L+G HDFT F +   +  S +R I   DV  
Sbjct: 119 EHTNPFMRKYSMHVGKKLNIENMQKAAQYLIGSHDFTAFSNAKSKKKSMVREIYMLDVVE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I+IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 179 SEGFIQIRVNGNGFLHNMVRKIVGALVEVGLGQLDAEVIPQILEAKQRNQINCLADASGL 238

Query: 240 YFDSVEY 246
           Y + V++
Sbjct: 239 YLEKVDF 245


>gi|323499722|ref|ZP_08104688.1| tRNA pseudouridine synthase A [Vibrio sinaloensis DSM 21326]
 gi|323315224|gb|EGA68269.1| tRNA pseudouridine synthase A [Vibrio sinaloensis DSM 21326]
          Length = 264

 Score =  167 bits (422), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 101/246 (41%), Positives = 136/246 (55%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ Y+GWQRQ+   S+Q ++EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTQYYGWQRQQEVKSVQEALEKALSVVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V      NA L  SD +++     V + FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTASRKMVAWTMGANANLP-SD-VAVRWAKEVPEDFHARFSATARRYRYIIFNSAL 118

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD + M  AAQ+L+G +DFT+FR+ HCQ+ SP R + H +V   
Sbjct: 119 RPGILSSGVS-HYHGELDEKKMHQAAQYLLGENDFTSFRATHCQSRSPWRNMMHINVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I + A +F+H  +R+  GSL  VG G+     +E  LQA+DRK  G  A  EGLY
Sbjct: 178 NQYVVIDIKANAFVHHMVRNITGSLICVGRGEQKPEWIEWLLQAKDRKLAGATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVDVDY 243


>gi|83645231|ref|YP_433666.1| tRNA pseudouridine synthase A [Hahella chejuensis KCTC 2396]
 gi|83633274|gb|ABC29241.1| tRNA pseudouridine synthase A [Hahella chejuensis KCTC 2396]
          Length = 283

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 132/246 (53%), Gaps = 5/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +++ Y+GS Y GWQ Q +G  S+Q  +E A+  V    V V  AGRTD+GVHA+ QV
Sbjct: 23  RVALVLGYDGSRYHGWQAQNSGVPSVQAEVESALAKVADHPVSVVCAGRTDAGVHAVNQV 82

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+      P      +N +L     +S+     V + FHAR++A  RSY Y I     
Sbjct: 83  VHFETKALRSPYSWAMGVNHFLPAD--VSVSWAGAVPEDFHARYTATSRSYRYVIYNHPI 140

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L     W   + LD E+M  A  HL+G +DF+ FR   CQ+ SP R +   +V+ F
Sbjct: 141 RPAWLNNSVTWNY-RPLDVESMSAAGAHLIGENDFSAFRGSDCQSKSPFRNLTRLEVSRF 199

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++ I V A +FLH  +R+  G+L  VG GK  S  +   L ++ R + G  APP GLY
Sbjct: 200 GDMVVIEVEANAFLHHMVRNISGTLMAVGTGKKPSDWVADVLASKKRSKAGVTAPPFGLY 259

Query: 241 FDSVEY 246
             SV Y
Sbjct: 260 LTSVTY 265


>gi|71906507|ref|YP_284094.1| tRNA pseudouridine synthase A [Dechloromonas aromatica RCB]
 gi|123774503|sp|Q47HQ7|TRUA_DECAR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|71846128|gb|AAZ45624.1| tRNA pseudouridine synthase [Dechloromonas aromatica RCB]
          Length = 262

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY G+G+ GWQ Q  G ++Q ++E A+  V G  V V  AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYCGTGFHGWQSQAGGGTVQDALEAALGEVAGVPVGVLCAGRTDAGVHATHQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           AHFD   +       + +N++L   + +++     V + FHARFSA  R Y Y ++ R  
Sbjct: 61  AHFDAPVDRPLTAWVRGVNSHL--PEGVAVRWAQPVAEDFHARFSARGRRYRYLLLNRPQ 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L +GR       L+ E M+ A   L+G HDF+ FR+ +CQA SP++ +   +V   G
Sbjct: 119 RPGLWQGRVGWFHWPLELEAMQEACLRLLGEHDFSAFRAANCQAKSPVKHMSRAEVRQCG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N+      A +FLH  +R+ VG+L  +G G      +E  LQ +DRK   P   P+GLYF
Sbjct: 179 NMFVFDFEASAFLHHMVRNLVGTLVYIGKGTQQPDWIEALLQTKDRKLAAPTFSPDGLYF 238

Query: 242 DSVEYS 247
               Y 
Sbjct: 239 RGPVYE 244


>gi|187929218|ref|YP_001899705.1| tRNA pseudouridine synthase A [Ralstonia pickettii 12J]
 gi|238689527|sp|B2U6Z1|TRUA_RALPJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|187726108|gb|ACD27273.1| tRNA pseudouridine synthase A [Ralstonia pickettii 12J]
          Length = 274

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 95/252 (37%), Positives = 143/252 (56%), Gaps = 10/252 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I+Y+G+ + GWQ Q +G+++Q ++E A+    G  +    AGRTD+GVHAL Q
Sbjct: 1   MTRIALGIQYDGAAFSGWQSQPHGNTVQDALESALRQFAGVALPTTVAGRTDAGVHALGQ 60

Query: 61  VAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII- 117
           V H D  LVRE  P    +  NA+L    T+++     + + FHARFSA RR+Y Y +  
Sbjct: 61  VVHLDTDLVRE--PFSWVRGTNAFLP--PTVAVRWAQEMPEDFHARFSAHRRTYYYALTF 116

Query: 118 -TRQAPLALEKGRAWLIP--KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
              +APL  +K    ++P  +SLD   M  AAQ LVG HDF++FR+  CQA SP++T+  
Sbjct: 117 GPTRAPLLEDKAGYVMLPPGQSLDVAAMNEAAQVLVGEHDFSSFRAAECQAKSPVKTMYS 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  + +R+   +FLH  +R+ +G L  +G G+   + +   L A+ R    P  
Sbjct: 177 IEVRGEGEWVFVRIRGSAFLHHMVRNIMGCLVAIGRGRQPVSWMGDVLAARSRVAAAPTF 236

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V Y
Sbjct: 237 MPDGLYLAEVGY 248


>gi|325266500|ref|ZP_08133177.1| tRNA pseudouridine synthase A [Kingella denitrificans ATCC 33394]
 gi|324981943|gb|EGC17578.1| tRNA pseudouridine synthase A [Kingella denitrificans ATCC 33394]
          Length = 265

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 140/245 (57%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           RY + + Y+GS +FGWQ+Q  G +++Q ++E A+  + GE V V  AGRTD+GVHA  QV
Sbjct: 8   RYALTLAYDGSRFFGWQKQAEGVATVQAALEHALSQIAGEPVSVIAAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       + +NA+L     +++    I D  FHARF A  R Y Y + +   
Sbjct: 68  VHFDSRADRPLSAWVRGVNAHLP--QGVAVHKAQIADSAFHARFDASGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L  GRA     +L+ + MR AAQ LVG HDF++FR+  CQA SP++T+    +   G
Sbjct: 126 RSPLLYGRAGWTHYALNDDAMRQAAQLLVGEHDFSSFRAAQCQAKSPVKTMYAVHLQRTG 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +L+++ + A +FLH  +R+ +G+L  VG G+ +     + ++ + R    P   P+GLY 
Sbjct: 186 SLLKLDLHANAFLHHMVRNIMGALVYVGCGRLSVAQFGELIETRSRLYAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|331000940|ref|ZP_08324577.1| tRNA pseudouridine synthase A [Parasutterella excrementihominis YIT
           11859]
 gi|329569899|gb|EGG51656.1| tRNA pseudouridine synthase A [Parasutterella excrementihominis YIT
           11859]
          Length = 259

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 135/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G  + GWQ Q +G ++Q  +E A+   TGE V    AGRTD+ VHA  QV
Sbjct: 1   MRVALGLEYDGRSFEGWQTQPSGQTVQDYLEAAVVQFTGEKVKAVCAGRTDANVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D   +   +   + LN+YL      ++    +V  +FHARFSA  R+Y Y I+    
Sbjct: 61  IHLDTGADRKEISWVRGLNSYLPTE--CAVRWAKVVPDEFHARFSACSRTYEYWIVNEPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GR   + + L+ +NM  A Q LVG HDF++FR+  CQ+ +P++ I++  V   G
Sbjct: 119 RSPILSGRTGWVFRPLNEKNMEAAGQFLVGEHDFSSFRAAGCQSKTPVKNIEYLHVIRLG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I+IRV A +FL+  +R+ VG L  VG G  +   + + L+A+ R+   P   P GLY 
Sbjct: 179 RFIKIRVKADAFLYHMVRNIVGCLVYVGTGARSVDWMGEVLEAKSRQAAAPTFYPTGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 TGVGY 243


>gi|302784784|ref|XP_002974164.1| hypothetical protein SELMODRAFT_100819 [Selaginella moellendorffii]
 gi|300158496|gb|EFJ25119.1| hypothetical protein SELMODRAFT_100819 [Selaginella moellendorffii]
          Length = 321

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 100/277 (36%), Positives = 151/277 (54%), Gaps = 33/277 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + IEY G+ + GWQRQ+   ++QG++E A     G+ V   G+ RTD+GVHALR V 
Sbjct: 29  RYLVGIEYIGTRFSGWQRQEGVRTVQGTLEDAFSSFMGQSVSTTGSSRTDAGVHALRNVF 88

Query: 63  HFDLVR-----------EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRR 110
           H DL R              P ++ +A+N +L + S  + +++   V   FHARF A  R
Sbjct: 89  HVDLARTSKRKPGELLAPHPPDVIVRAVNHFLQRESADVQVVDARFVPPDFHARFRAKER 148

Query: 111 SYLYRIITRQAPLAL-EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YRI+      +L E+ RAW + + L+   M+ A Q L+G HDF++FR+  CQA+SP+
Sbjct: 149 TYYYRILAGSCRASLFERDRAWHVEEPLNLIAMQSACQVLLGTHDFSSFRASGCQAASPV 208

Query: 170 RTIDHFDV------------------NSFGNLIEIRVVAR--SFLHTQIRSFVGSLKLVG 209
           +T++   +                  +S  +L    V AR  SFL+ Q+R  VG+LK VG
Sbjct: 209 KTLEELSIRETVSWPHLLTGCSSNAQSSNPDLKSYVVTARAQSFLYHQVRLMVGTLKGVG 268

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            GK T+ D+ K L+ +      P+AP  GL+   V+Y
Sbjct: 269 AGKRTAEDVRKILEGRSISLALPMAPASGLFLADVKY 305


>gi|71892269|ref|YP_278003.1| tRNA pseudouridine synthase A [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
 gi|123775274|sp|Q492H3|TRUA_BLOPB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|71796375|gb|AAZ41126.1| tRNA pseudouridine synthase A [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 261

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 101/246 (41%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + IEY+GS Y GWQRQ++  SIQ  IE AI  +T E V V  AGRTDSGVHAL Q
Sbjct: 1   MQKLALGIEYDGSWYCGWQRQRDAPSIQSYIENAIKKITSESVTVFCAGRTDSGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+             +N YL    +I +    +V+K FHARFSAI R Y Y I    
Sbjct: 61  VVHFETYSRRSKSAWTLGMNRYLP--SSICVRWARLVNKDFHARFSAISRRYCYIINNNC 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL   + W   K LD   M  AAQ+L+G +DF++FR+  CQ+ S  R + H  +   
Sbjct: 119 IRSALLFRKTWHYKKYLDINKMCDAAQYLLGENDFSSFRAAGCQSYSARRKLYHIRIIRK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I I + A SF++  +R+ VGSL  VG G+     + + L+  +R   G  AP  GLY
Sbjct: 179 GQCIVIDIKANSFMYRMVRNIVGSLVKVGCGEQPEKWIAELLENCNRSLAGVTAPASGLY 238

Query: 241 FDSVEY 246
              V+Y
Sbjct: 239 LVEVKY 244


>gi|156933088|ref|YP_001437004.1| tRNA pseudouridine synthase A [Cronobacter sakazakii ATCC BAA-894]
 gi|166228697|sp|A7MH65|TRUA_ENTS8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|156531342|gb|ABU76168.1| hypothetical protein ESA_00898 [Cronobacter sakazakii ATCC BAA-894]
          Length = 270

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 98/248 (39%), Positives = 140/248 (56%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +++  + IEY+GS Y+GWQRQ+   S+Q  +EKA+  V  E + V  AGRTD+GVHA  Q
Sbjct: 9   VVKIALGIEYDGSKYYGWQRQQEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHATGQ 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-R 119
           V HF+             +NA L     I++  +  V  +FHARFSA  R Y Y I   R
Sbjct: 69  VVHFETTAIRKDAAWTLGVNANL--PGDIAVRWVKDVPAEFHARFSATARRYRYVIYNHR 126

Query: 120 QAPLALEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
             P  L +G   + +P  LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V 
Sbjct: 127 LRPAVLSQGVTHYHLP--LDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNLMHINVE 184

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            FG  I + + A +F+H  +R+ VGSL  +G G    + + + L A+DR      A  EG
Sbjct: 185 RFGAYIVVDIKANAFVHHMVRNIVGSLMEIGCGNQPESWMAELLAAKDRTLAAATAKAEG 244

Query: 239 LYFDSVEY 246
           LY  SV+Y
Sbjct: 245 LYLVSVDY 252


>gi|229101230|ref|ZP_04231994.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock3-28]
 gi|228682198|gb|EEL36311.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock3-28]
          Length = 245

 Score =  166 bits (421), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MHNYKLTIQYDGARYKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFKSDEKLVEHKVKKYLNQYL--PNDISITNVEEVPDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ E+M+ AA+HLVG HDFT F +   +  S +R +   +V+ 
Sbjct: 119 EHTNPFMRKHSMHVNKKLNVESMKKAAKHLVGSHDFTAFSNAKSKKKSMVREVYMLEVSE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDADAIPNILEEKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y +S+E+
Sbjct: 239 YLESIEF 245


>gi|53803316|ref|YP_114909.1| tRNA pseudouridine synthase A [Methylococcus capsulatus str. Bath]
 gi|62901252|sp|Q604P1|TRUA_METCA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|53757077|gb|AAU91368.1| tRNA pseudouridine synthase A [Methylococcus capsulatus str. Bath]
          Length = 271

 Score =  166 bits (421), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/250 (38%), Positives = 132/250 (52%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GSG+ GWQ Q    +IQ  +E+A+  V    V V  AGRTD+GVHA+ QV
Sbjct: 1   MRIALGIEYDGSGFAGWQWQNGKRTIQAEVERALSRVADAPVRVTCAGRTDAGVHAIEQV 60

Query: 62  AHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AHFD       R W+       L A   + + + IL +   +  FHAR SAI R Y Y I
Sbjct: 61  AHFDTESRRSERSWL-------LGANTALPEDVRILWVRETEPHFHARLSAIARYYRYEI 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           + R    AL   +       LD E MR  A +LVG HDF++FR+  CQ+ SP R +    
Sbjct: 114 LNRPMRSALRPRQFTWCHAPLDVERMREGAAYLVGEHDFSSFRAQQCQSRSPFRRVHFLH 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + + + A +F+H  +R+  G L  VG GK     + + L  +DR + G  APP
Sbjct: 174 VRREGERVIMEIAANAFVHHMVRNIAGVLMAVGAGKRDPAWVGELLAMRDRAKGGVTAPP 233

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 234 DGLYLGGVCY 243


>gi|77164531|ref|YP_343056.1| pseudouridylate synthase [Nitrosococcus oceani ATCC 19707]
 gi|254433109|ref|ZP_05046617.1| tRNA pseudouridine synthase A [Nitrosococcus oceani AFC27]
 gi|123594636|sp|Q3JCC0|TRUA_NITOC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|76882845|gb|ABA57526.1| Pseudouridylate synthase [Nitrosococcus oceani ATCC 19707]
 gi|207089442|gb|EDZ66713.1| tRNA pseudouridine synthase A [Nitrosococcus oceani AFC27]
          Length = 259

 Score =  166 bits (421), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/250 (38%), Positives = 135/250 (54%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+GS + GWQ QK   ++Q ++E+A+  V  E V V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGLEYDGSNFSGWQSQKGVRTVQATLEQALSAVANEPVTVITAGRTDAGVHAAAQV 60

Query: 62  AHFD-----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD     L   WV             +   ++IL    V++ FHARFSAI R Y Y I
Sbjct: 61  VHFDTATFRLEHNWV-------FGGNANLLPEVAILWAQPVNEAFHARFSAIARHYRYII 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           + R A  A+   R     + L    M+ A   LVG HDF++FR+  CQA SP+R + + +
Sbjct: 114 LNRGARPAIANRRVTWYCQPLSVTKMKEAGAFLVGEHDFSSFRAKACQAKSPVRNVHYLE 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G+ I I + A +FLH  +R+  G L  +G G+      E+ LQA+ R   G  A P
Sbjct: 174 VTRQGDWIVIDISANAFLHHMVRNIAGVLMAIGKGEQPPRWAEEVLQARCRAVGGVTARP 233

Query: 237 EGLYFDSVEY 246
           +GLY   V+Y
Sbjct: 234 DGLYLVRVDY 243


>gi|237748866|ref|ZP_04579346.1| tRNA pseudouridine synthase A [Oxalobacter formigenes OXCC13]
 gi|229380228|gb|EEO30319.1| tRNA pseudouridine synthase A [Oxalobacter formigenes OXCC13]
          Length = 261

 Score =  166 bits (421), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 93/248 (37%), Positives = 132/248 (53%), Gaps = 1/248 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+G+ + GWQ Q +G ++Q  +++AIF  T   +    AGRTD+GVHA  Q
Sbjct: 1   MKRIALGIEYDGTNWRGWQTQPDGMTVQDQLQEAIFRFTRTRISTMCAGRTDAGVHASEQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTIS-ILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           V H D   + +PV   + +NAYL  S  +     +      FHAR SA+ R Y Y I   
Sbjct: 61  VVHLDTELDRLPVSWVRGVNAYLPSSIAVRWACEVPGGKDGFHARSSAMARRYRYLIYNS 120

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L K RA  + K LD   M+  A  L+G HDF+ FR+  CQ+ +P++T+   D+  
Sbjct: 121 PVRSPLWKNRAGWVFKPLDIGLMQKGAGLLLGEHDFSAFRAAECQSITPVKTVKRIDIEK 180

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GNLI     A +FLH  +R+ VGSL  +G G      +++ L A+DR    P   P+GL
Sbjct: 181 QGNLIVFTFEANAFLHHMVRNIVGSLVYIGKGNHPPEWMKQLLDAKDRSLAAPTFMPDGL 240

Query: 240 YFDSVEYS 247
           Y   V Y 
Sbjct: 241 YLSRVHYE 248


>gi|148977676|ref|ZP_01814237.1| tRNA pseudouridine synthase A [Vibrionales bacterium SWAT-3]
 gi|145963044|gb|EDK28313.1| tRNA pseudouridine synthase A [Vibrionales bacterium SWAT-3]
          Length = 264

 Score =  166 bits (420), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 138/246 (56%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG+ YFGWQRQ++  S+Q  +EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MKIALGIEYNGTHYFGWQRQRDVKSVQEELEKALSVVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +   V      NA   +   I++   + V++ FHARFSA  R Y Y I     
Sbjct: 61  VHFETNVDRKMVAWTMGANA--NMPKDIAVRWATEVNEDFHARFSATARRYRYIIFNHAL 118

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD + M  A Q+L+G +DFT+FR+ HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGHLDEKKMHEAGQYLLGENDFTSFRATHCQSHSPWRNMIHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY
Sbjct: 178 GHYIVIDIKANAFVHHMVRNITGSLIAVGKGEQKPEWIKWLLEAKDRKLAGATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVDVDY 243


>gi|228989617|ref|ZP_04149601.1| tRNA pseudouridine synthase A 2 [Bacillus pseudomycoides DSM 12442]
 gi|228770154|gb|EEM18734.1| tRNA pseudouridine synthase A 2 [Bacillus pseudomycoides DSM 12442]
          Length = 245

 Score =  166 bits (420), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 141/247 (57%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G  Y GWQR   N ++IQG IE  +  +TG  + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGGRYKGWQRLGNNDNTIQGKIESVLSEMTGREIEIIGCSRTDAGVHALH 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F +      + + K LN YL   + ISI ++ ++ ++FHAR+++  ++YLY+I   
Sbjct: 61  QVANFKIDENLPELKVKKYLNQYL--PNDISITDVELISERFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ENM+ AAQ+L+G HDFT F +   +  S +R I   DV  
Sbjct: 119 EHTNPFMRKYSMHVGKKLNIENMQKAAQYLIGSHDFTAFSNAKSKKKSMVREIYMLDVVE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I+IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 179 SEGFIQIRVNGNGFLHNMVRKIVGALVEVGLGQLDAEVIPQILEAKQRNQINCLADASGL 238

Query: 240 YFDSVEY 246
           Y + V++
Sbjct: 239 YLEKVDF 245


>gi|304388653|ref|ZP_07370715.1| tRNA pseudouridine synthase A [Neisseria meningitidis ATCC 13091]
 gi|304337399|gb|EFM03571.1| tRNA pseudouridine synthase A [Neisseria meningitidis ATCC 13091]
          Length = 265

 Score =  166 bits (420), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|170718977|ref|YP_001784140.1| tRNA pseudouridine synthase A [Haemophilus somnus 2336]
 gi|189030135|sp|B0USP1|TRUA_HAES2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|168827106|gb|ACA32477.1| tRNA pseudouridine synthase A [Haemophilus somnus 2336]
          Length = 269

 Score =  166 bits (420), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 99/252 (39%), Positives = 135/252 (53%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG+ YFGWQRQ N +S+Q  +E A+  V  E   ++ AGRTDSGVHA  QV
Sbjct: 1   MKIALGIEYNGTHYFGWQRQANVTSVQEKLESAVSFVANEFCQIYCAGRTDSGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             LNA L     I++    +V + FHARFSA  R Y Y I     
Sbjct: 61  VHFDTKAIRSEKAWTFGLNANLPAD--IAVRWAKVVSEDFHARFSATARRYRYLIYNH-- 116

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           PL     R+ L P        +LD   M  A Q+L+G HDF++FR+  CQ+++P R I H
Sbjct: 117 PL-----RSALFPTGVTHHHVALDHHLMHQAGQYLLGEHDFSSFRAAQCQSNTPWRNIHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V    N I + + A +F+H  +R+ VGSL  +G GK     ++  L  +DR    P A
Sbjct: 172 LHVFRQANYIIVDIQANAFVHHMVRNIVGSLLEIGSGKQPVEWMDWLLTQKDRTLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V+Y
Sbjct: 232 KPDGLYLVEVKY 243


>gi|198283837|ref|YP_002220158.1| tRNA pseudouridine synthase A [Acidithiobacillus ferrooxidans ATCC
           53993]
 gi|218666580|ref|YP_002426474.1| tRNA pseudouridine synthase A [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|198248358|gb|ACH83951.1| tRNA pseudouridine synthase A [Acidithiobacillus ferrooxidans ATCC
           53993]
 gi|218518793|gb|ACK79379.1| tRNA pseudouridine synthase A [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 271

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 96/244 (39%), Positives = 131/244 (53%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R+ + +EY+G+G+ GWQRQ +  S+QG +E A+  V    + V  AGRTD+GVHAL QV 
Sbjct: 11  RWALGLEYDGNGFCGWQRQLDQDSVQGVVEAALSRVAQCPISVVVAGRTDTGVHALCQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD      P    +  N  L     +++    +V   FHARFSA  R Y Y I+ R+  
Sbjct: 71  HFDSPVLRRPEAWVRGANTALPAG--VALRWARVVPDSFHARFSATARRYRYVILNRREK 128

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            AL +     I   LD E M+ AAQ L+G HDF+ FR+  CQA SP+R +    V   G+
Sbjct: 129 SALWRNHTAWIYSPLDVEAMQAAAQTLLGTHDFSAFRAAACQAKSPVRNLCQLRVVRRGD 188

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           LI +   A  FLH  +R+ VG L  +G          + L ++DR   G  APP GLYF 
Sbjct: 189 LIAVDAEANGFLHHMVRNLVGVLIAIGKADRPVDWAAEVLASRDRCRAGVTAPPGGLYFV 248

Query: 243 SVEY 246
           +  Y
Sbjct: 249 APRY 252


>gi|254804153|ref|YP_003082374.1| tRNA pseudouridine synthase A [Neisseria meningitidis alpha14]
 gi|254667695|emb|CBA03553.1| tRNA pseudouridine synthase A [Neisseria meningitidis alpha14]
          Length = 265

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGESVATTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTAAARPQQAWIRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRQAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|218767391|ref|YP_002341903.1| tRNA pseudouridine synthase A [Neisseria meningitidis Z2491]
 gi|25009506|sp|Q9JWF1|TRUA_NEIMA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|121051399|emb|CAM07691.1| tRNA pseudouridine synthase [Neisseria meningitidis Z2491]
          Length = 265

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|295109363|emb|CBL23316.1| pseudouridylate synthase I [Ruminococcus obeum A2-162]
          Length = 246

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 91/246 (36%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG +IQG +  A+  + GE + + GA RTD+GVHAL  
Sbjct: 1   MKRVGLVVAYDGTNYSGWQIQPNGITIQGVLNDALSDLLGEKIEIMGASRTDAGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  ALN   ++ + I I     V+  FH R+    ++Y YRI+ R+
Sbjct: 61  VAVFDTNTRIPGEKISYALNQ--RLPEDIRIQLSEEVEPDFHPRYCDSEKTYEYRILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  E+  ++     LD E MR A  +L+GRHDF +F     Q  S +RTI   DV   
Sbjct: 119 FPVPTERLYSYFYHYKLDIEKMREATSYLIGRHDFASFCGTGAQVKSTVRTITGIDVWRD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++ IRV    FL+  +R   G+L  VG+G++    ++K L A DR   GP AP  GL 
Sbjct: 179 GDIVTIRVKGEGFLYNMVRIIAGTLIQVGNGQYPPERVKKILDACDRSVSGPTAPAHGLT 238

Query: 241 FDSVEY 246
              +E+
Sbjct: 239 LMGIEF 244


>gi|167840379|ref|ZP_02467063.1| tRNA pseudouridine synthase A [Burkholderia thailandensis MSMB43]
          Length = 270

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q S+E A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQSQPHGKTVQDSLEAALAEFAQTSLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       +  NA+L    TI++     +   FHARF+A  R+Y Y +     
Sbjct: 61  VHFDTDLDRADFSWVRGTNAFLP--STIAVQWAKPMPDTFHARFAAYERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GR   +   LD + MR AA HLVG HDF+ FRS  CQA SP++ +    +   G
Sbjct: 119 RSPMLAGRTGWVHTPLDIDAMREAAGHLVGEHDFSAFRSSECQAKSPVKHLYQIGIRPDG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I  R  A +FLH  +R+ +G L  VG G++ ++ L   L+++DR    P   PEGLY 
Sbjct: 179 DFIHFRFRASAFLHHMVRNLMGCLVAVGRGRYPASWLADVLESRDRDCAAPTFMPEGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 AHVGY 243


>gi|186473191|ref|YP_001860533.1| tRNA pseudouridine synthase A [Burkholderia phymatum STM815]
 gi|238691329|sp|B2JQE6|TRUA_BURP8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|184195523|gb|ACC73487.1| tRNA pseudouridine synthase A [Burkholderia phymatum STM815]
          Length = 267

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 90/248 (36%), Positives = 133/248 (53%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + I+Y+G+ + GWQ Q +G ++Q  +E+A+  F +T    VV  AGRTD+GVH L
Sbjct: 1   MTRIALGIQYDGAAFCGWQSQPHGKTVQDELERALREFALTPLQTVV--AGRTDTGVHGL 58

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV HFD   +       +  NA+L    T+++     +   FHARFSA  R+Y Y +  
Sbjct: 59  GQVVHFDTELDRAEFSWVRGTNAFLP--STVAVQWAKPMPDAFHARFSAFERTYYYALYV 116

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
                 +   RA  I   LD + MR AA  L+G HDF+ FRS  CQ+ +P++ +   D+ 
Sbjct: 117 HPVRSPMLASRAGWIHTPLDVDAMREAAACLIGEHDFSAFRSSECQSKTPVKHLYQIDIR 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+ I  R  A +FLH  +R+ +G L  VG G++ +  L + L  +DR    P   P+G
Sbjct: 177 PQGDFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPAAWLSEVLHGRDRNRAAPTFMPDG 236

Query: 239 LYFDSVEY 246
           LY   V Y
Sbjct: 237 LYLAQVGY 244


>gi|296159699|ref|ZP_06842522.1| tRNA pseudouridine synthase A [Burkholderia sp. Ch1-1]
 gi|295890143|gb|EFG69938.1| tRNA pseudouridine synthase A [Burkholderia sp. Ch1-1]
          Length = 270

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + ++Y+GS + GWQ Q +G+++Q  +E+A+       V    AGRTD+GVH L Q
Sbjct: 1   MKRIALGVQYDGSAFCGWQSQPHGNTVQDELERALREFAQTPVQTIVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +   V   +  N++L    TIS+     +  +FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTEIDRADVSWVRGTNSFLP--KTISVQWAKPMPDEFHARFSAFERTYYYVLYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   RA  +  +LD + M+ AA HL+G HDF+ FRS  CQ+ +PI+ +   DV   
Sbjct: 119 VRSPMLATRAGWVHTALDVDAMQAAAAHLIGEHDFSAFRSSQCQSKTPIKHLHQIDVRQH 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +  R  A +FLH  +R+ +G L  +G G+     + + L ++DR    P   P+GLY
Sbjct: 179 GDFVHFRFRANAFLHHMVRNLMGCLVYIGRGRRPVEWMAEVLASRDRDFAAPTFMPDGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAQVGY 244


>gi|189220286|ref|YP_001940926.1| pseudouridylate synthase [Methylacidiphilum infernorum V4]
 gi|259550415|sp|B3E0A0|TRUA_METI4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189187144|gb|ACD84329.1| Pseudouridylate synthase [Methylacidiphilum infernorum V4]
          Length = 255

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 94/249 (37%), Positives = 145/249 (58%), Gaps = 5/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++ Y + + Y GSG+ GWQRQ    ++Q ++E+A+  +  E + V GAGRTD+GVHA  Q
Sbjct: 5   VVGYKLTLSYCGSGFHGWQRQGELPTVQRALEEAVAKIWEEPIPVEGAGRTDAGVHAKGQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F   R+  P +L +ALN +L   DT+ + +  IV ++F ARF A+ ++Y Y +    
Sbjct: 65  VASFAAPRKLEPEVLKRALNYHL--PDTVRVWDARIVPREFSARFDAVSKTYQYLLWNDP 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQASSPIRTI-DHFDVN 178
                  GRAW IP+++D E M  AA+  +G+H+F  F S       +P+RT+ D F + 
Sbjct: 123 VMDPFYLGRAWHIPRAMDVEMMNEAARLFLGKHNFAAFVSNPGMPVKNPVRTVLDCFFLE 182

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G+L+   V A  FL+  +R+ VG+L  VG G+ +  +L+K  + Q R E    APP G
Sbjct: 183 Q-GSLVFFNVKADGFLYRMVRNMVGALVKVGLGRLSRQELKKIFENQKRIEAFAAAPPWG 241

Query: 239 LYFDSVEYS 247
           LY  +V+Y 
Sbjct: 242 LYLLAVDYP 250


>gi|113461401|ref|YP_719470.1| tRNA pseudouridine synthase A [Haemophilus somnus 129PT]
 gi|122945393|sp|Q0I4X5|TRUA_HAES1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|112823444|gb|ABI25533.1| pseudouridylate synthetase [Haemophilus somnus 129PT]
          Length = 269

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 99/252 (39%), Positives = 135/252 (53%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG+ YFGWQRQ N +S+Q  +E A+  V  E   ++ AGRTDSGVHA  QV
Sbjct: 1   MKIALGIEYNGTHYFGWQRQANVTSVQEKLESAVSFVANEFCQIYCAGRTDSGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             LNA L     I++    +V + FHARFSA  R Y Y I     
Sbjct: 61  VHFDTKAIRSEKAWTFGLNANLPAD--IAVRWAKVVSEDFHARFSATARRYRYLIYNH-- 116

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           PL     R+ L P        +LD   M  A Q+L+G HDF++FR+  CQ+++P R I H
Sbjct: 117 PL-----RSALFPTGVTHHHVALDHRLMHQAGQYLLGEHDFSSFRAAQCQSNTPWRNIHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V    N I + + A +F+H  +R+ VGSL  +G GK     ++  L  +DR    P A
Sbjct: 172 LHVFRQANYIIVDIQANAFVHHMVRNIVGSLLEIGSGKQPVEWMDWLLTQKDRTLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V+Y
Sbjct: 232 KPDGLYLVEVKY 243


>gi|325131279|gb|EGC53990.1| tRNA pseudouridine synthase A [Neisseria meningitidis M6190]
 gi|325137309|gb|EGC59897.1| tRNA pseudouridine synthase A [Neisseria meningitidis ES14902]
 gi|325139358|gb|EGC61898.1| tRNA pseudouridine synthase A [Neisseria meningitidis CU385]
          Length = 265

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSS 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|319943971|ref|ZP_08018251.1| tRNA pseudouridine synthase A [Lautropia mirabilis ATCC 51599]
 gi|319742732|gb|EFV95139.1| tRNA pseudouridine synthase A [Lautropia mirabilis ATCC 51599]
          Length = 307

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 90/250 (36%), Positives = 138/250 (55%), Gaps = 8/250 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKN----GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL 58
           R+   + Y+G  + GWQ+Q        S+Q ++E A+  V G+ + +  AGRTD+GVHAL
Sbjct: 41  RWVCGVSYDGRDFCGWQKQPPVPGLAPSVQTTVEAALSAVAGQTIDIRCAGRTDAGVHAL 100

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIV--DKQFHARFSAIRRSYLYRI 116
            QV  F    +  P    +  NA+L   DT+++   + +  D  F ARFSA  R+Y Y +
Sbjct: 101 EQVIEFSTTAQRPPTAWVRGANAHLP--DTVAVRWAAPLAPDADFDARFSARERTYWYVL 158

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           I       L +GRA    + LD   M+ AA+ ++G HDF++FR+  CQA++P+RT+  + 
Sbjct: 159 IDSPVAPPLWQGRAGWTHRPLDVARMQAAARSVLGTHDFSSFRASECQAATPVRTLTEWT 218

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + +R+ A +FLH  +R+ VGSL  VGDG+   + + + L A+ R    P    
Sbjct: 219 VERHGAFVMMRLTANAFLHHMVRNLVGSLVYVGDGRRPVSWMAEVLAARSRSAGAPTFAA 278

Query: 237 EGLYFDSVEY 246
            GLY  SV Y
Sbjct: 279 GGLYLASVRY 288


>gi|84394308|ref|ZP_00993032.1| tRNA pseudouridine synthase A [Vibrio splendidus 12B01]
 gi|84375076|gb|EAP91999.1| tRNA pseudouridine synthase A [Vibrio splendidus 12B01]
          Length = 264

 Score =  166 bits (419), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 138/246 (56%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG+ YFGWQRQ++  S+Q  +EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MKIALGIEYNGTHYFGWQRQRDVKSVQEELEKALSVVANHPVEVMCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +   V      NA   +   I++   + V++ FHARFSA  R Y Y I     
Sbjct: 61  VHFETNVDRKMVAWTMGANA--NMPKDIAVRWATEVNEDFHARFSATARRYRYIIFNHAL 118

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD + M  A Q+L+G +DFT+FR+ HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGHLDEKKMHEAGQYLLGENDFTSFRATHCQSRSPWRNMIHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY
Sbjct: 178 GHYIVIDIKANAFVHHMVRNITGSLIAVGKGEQKPEWIQWLLEAKDRKVAGATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVDVDY 243


>gi|127513234|ref|YP_001094431.1| tRNA pseudouridine synthase A [Shewanella loihica PV-4]
 gi|166229835|sp|A3QFC4|TRUA_SHELP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|126638529|gb|ABO24172.1| tRNA pseudouridine synthase A [Shewanella loihica PV-4]
          Length = 261

 Score =  166 bits (419), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 135/247 (54%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ    S+Q  +E+A+  V  E + +  AGRTD+GVHA  QV
Sbjct: 1   MRVALGIEYDGSRYFGWQRQAEVDSVQAQLERALSFVANEPISIQCAGRTDAGVHATGQV 60

Query: 62  AHFDL--VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            HF+   VR+     L   +N    + D I++     VD +FHARF+A  R Y Y I   
Sbjct: 61  VHFETNAVRKESAWTLGVNVN----LPDDIAVRWAKDVDDEFHARFTATARRYRYMIYNH 116

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q    + +      P  +D   M  AAQ L+G  DFT+FR+I CQ+++P R +   +V  
Sbjct: 117 QFRPGILRSGVSHYPGQIDEAKMHEAAQFLLGEQDFTSFRAIQCQSNTPFRCVHEVNVTR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I + + A +FLH  +R+ VGSL  VG G+   + +++ L  +DR +    A P GL
Sbjct: 177 QGMYICVDIKANAFLHHMVRNIVGSLLEVGYGRQPVSWIKELLALKDRTQAAATAKPNGL 236

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 237 YLVDVTY 243


>gi|261393361|emb|CAX50997.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I; tRNA
           pseudouridylate synthase I) [Neisseria meningitidis
           8013]
          Length = 265

 Score =  166 bits (419), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSS 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|150392126|ref|YP_001322175.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
 gi|149951988|gb|ABR50516.1| tRNA pseudouridine synthase A [Alkaliphilus metalliredigens QYMF]
          Length = 255

 Score =  166 bits (419), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 137/246 (55%), Gaps = 3/246 (1%)

Query: 2   IRYCMI-IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  MI IEY+G+ Y GWQ Q+N  SIQ  I KA+  VTGE +  HG+GRTD+GVHA  Q
Sbjct: 1   MRNIMIEIEYDGTNYSGWQIQQNAPSIQEEIAKALKKVTGEEITTHGSGRTDAGVHAQGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA F L  +     +  ALN   K+   I+IL    + + FHAR+SAI + Y Y I+   
Sbjct: 61  VASFQLHSKIPAERISFALNG--KLPRDITILEAKEMPEDFHARYSAIGKRYGYCIMNNT 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL +   + +P  LD + M+ A++ L+G HDF  F +   Q  S +R ID  + ++ 
Sbjct: 119 HGSALLRNYCYHVPYKLDLQKMKQASETLLGTHDFKGFMASGSQVKSTVRRIDEINFDTQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I +    FL+  +R  VGSL  +G GK     L+  L+ Q+R+     AP +GLY
Sbjct: 179 GSQIWITMQGNGFLYKMVRIIVGSLVGIGTGKIKEEALQNILETQNRRVAVKTAPAQGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LQKVFY 244


>gi|260598738|ref|YP_003211309.1| tRNA pseudouridine synthase A [Cronobacter turicensis z3032]
 gi|260217915|emb|CBA32500.1| tRNA pseudouridine synthase A [Cronobacter turicensis z3032]
          Length = 262

 Score =  166 bits (419), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 99/248 (39%), Positives = 139/248 (56%), Gaps = 6/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + IEY+GS Y+GWQRQ+   S+Q  +EKA+  V  E V V  AGRTD+GVHA  Q
Sbjct: 1   MRKIALGIEYDGSKYYGWQRQQEVRSVQEKLEKALSQVANEPVNVFCAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-R 119
           V HF+             +NA L     I++  +  V  +FHARFSA  R Y Y I   R
Sbjct: 61  VVHFETTAVRKDAAWTLGVNANL--PGDIAVRWVKDVPAEFHARFSATARRYRYVIYNHR 118

Query: 120 QAPLALEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
             P  L +G   + +P  LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V 
Sbjct: 119 LRPAVLSQGVTHYHLP--LDAQRMHRAAQCLIGENDFTSFRAVQCQSRTPWRNLMHINVE 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            FG  I + + A +F+H  +R+ VGSL  +G G    + + + L A+DR      A  EG
Sbjct: 177 RFGAYIVVDIKANAFVHHMVRNIVGSLMEIGCGNQPESWMAELLAAKDRTLAAATAKAEG 236

Query: 239 LYFDSVEY 246
           LY  SV+Y
Sbjct: 237 LYLVSVDY 244


>gi|229159574|ref|ZP_04287588.1| tRNA pseudouridine synthase A 2 [Bacillus cereus R309803]
 gi|228623876|gb|EEK80688.1| tRNA pseudouridine synthase A 2 [Bacillus cereus R309803]
          Length = 250

 Score =  166 bits (419), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MYNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           Q+A+F    + V   + K LN YL   + ISI N+  V ++FHAR+++  ++YLY+I   
Sbjct: 66  QIANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHERFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ E+M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVESMKQAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEGKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|228913175|ref|ZP_04076814.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228846580|gb|EEM91593.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 250

 Score =  165 bits (418), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 141/247 (57%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLAAEAIPQILEAKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|302388745|ref|YP_003824566.1| tRNA pseudouridine synthase A [Thermosediminibacter oceani DSM
           16646]
 gi|302199373|gb|ADL06943.1| tRNA pseudouridine synthase A [Thermosediminibacter oceani DSM
           16646]
          Length = 243

 Score =  165 bits (418), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 92/242 (38%), Positives = 134/242 (55%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++EY+G+ Y GWQ+Q N  S+Q  +EKAI+ +TGE V + GAGRTD+GVHA  QVA+F 
Sbjct: 5   ILLEYDGTNYHGWQKQNNALSVQEVLEKAIYALTGERVSIIGAGRTDAGVHARGQVANFR 64

Query: 66  LVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
                +PV  L  A+N+  K+ + I++     V   FHAR+SA  + Y Y I     P  
Sbjct: 65  -TNTRIPVERLPYAINS--KLPEDIAVKGAEAVPDDFHARYSAKAKVYTYSIYNAPFPSP 121

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L +  ++  P  LD E MR AA+  +G HDF  FR+      + +R I   DV   G L+
Sbjct: 122 LLRRYSYFFPLPLDVEAMRRAAKAFIGVHDFAAFRASGSSVKTSVRNITRLDVKKCGKLL 181

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I V A  FL+  +R   G+L  VG GK    ++   ++++DR+  G   P  GL  + V
Sbjct: 182 TIEVEADGFLYNMVRIIAGTLLEVGTGKKDPEEIPSIIESRDRERAGVTLPAHGLCLEKV 241

Query: 245 EY 246
            Y
Sbjct: 242 IY 243


>gi|325133363|gb|EGC56028.1| tRNA pseudouridine synthase A [Neisseria meningitidis M13399]
          Length = 265

 Score =  165 bits (418), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALENALAQIAGEAVSTIVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWIRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|257464802|ref|ZP_05629173.1| tRNA pseudouridine synthase A [Actinobacillus minor 202]
 gi|257450462|gb|EEV24505.1| tRNA pseudouridine synthase A [Actinobacillus minor 202]
          Length = 262

 Score =  165 bits (418), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 98/252 (38%), Positives = 138/252 (54%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ++  S+Q  +E+A+ +V    V V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQESVESVQQKLEEALSIVANSPVEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +      C   NA+L   D I++     V + FHARFSA  R Y Y I  R  
Sbjct: 61  VHFETEAKRPLQAWCFGTNAHL--PDDIAVKWAVEVPEDFHARFSATARRYRYIIFNR-- 116

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
                K R+ ++PK        LD E M  A Q+L+G +DF++FR+  CQ+ +P R I H
Sbjct: 117 -----KLRSAILPKGVSHYHVDLDHEKMHEAGQYLLGENDFSSFRAAKCQSHTPWRNIHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V+  G  I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A
Sbjct: 172 LNVSRLGAYIIVDIQANAFVHHMVRNIVGSLIEVGQGNQPPEWIKWLLEQKDRTLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
             EGLY   V Y
Sbjct: 232 KAEGLYLVDVHY 243


>gi|269962161|ref|ZP_06176515.1| tRNA pseudouridine synthase A [Vibrio harveyi 1DA3]
 gi|269833245|gb|EEZ87350.1| tRNA pseudouridine synthase A [Vibrio harveyi 1DA3]
          Length = 264

 Score =  165 bits (418), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 95/245 (38%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ YFGWQRQ++  S+Q  +EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTNYFGWQRQRDVKSVQEELEKALSVVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V      NA   +   I++     V+  FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNVSRKMVAWTMGANA--NMPSDIAVRWAVEVNDDFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q+L+G +DF++FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDEKKMHEAGQYLLGENDFSSFRAAHCQSLSPFRNLMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 DYIVIDIKANAFVHHMVRNITGSLIKVGRGEEKPEWIKWLLEAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|153834426|ref|ZP_01987093.1| tRNA pseudouridine synthase A [Vibrio harveyi HY01]
 gi|156975370|ref|YP_001446277.1| tRNA pseudouridine synthase A [Vibrio harveyi ATCC BAA-1116]
 gi|166229849|sp|A7MS76|TRUA_VIBHB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|148869197|gb|EDL68225.1| tRNA pseudouridine synthase A [Vibrio harveyi HY01]
 gi|156526964|gb|ABU72050.1| hypothetical protein VIBHAR_03101 [Vibrio harveyi ATCC BAA-1116]
          Length = 264

 Score =  165 bits (418), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 95/245 (38%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ YFGWQRQ+   S+Q  +EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTNYFGWQRQREVKSVQEELEKALSVVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V      NA   +   I++     V+  FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNVSRKMVAWTMGANA--NMPSDIAVRWAVEVNDDFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q+L+G +DF++FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDEKKMHEAGQYLLGENDFSSFRAAHCQSLSPCRNMMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 DYIVIDIKANAFVHHMVRNITGSLIKVGRGEEKPEWIKSLLEAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|270262840|ref|ZP_06191111.1| tRNA pseudouridine synthase A [Serratia odorifera 4Rx13]
 gi|270043524|gb|EFA16617.1| tRNA pseudouridine synthase A [Serratia odorifera 4Rx13]
          Length = 273

 Score =  165 bits (418), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 138/246 (56%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+  +S+Q S+E+A+  V    + V  AGRTD+GVHA  QV
Sbjct: 12  LKIALGIEYDGSRYYGWQRQQEVASVQASLEQALSKVANAPISVLCAGRTDAGVHATGQV 71

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF+   +         +N +L     I++  ++ V + FHARFSA  R Y Y I   R 
Sbjct: 72  VHFETTAQRKDAAWTMGVNTHL--PPDIAVRWVTGVAEDFHARFSATARRYRYIIYNHRY 129

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L++G        LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V  +
Sbjct: 130 RPAVLQQGVTHFY-HPLDAERMERAAQALLGENDFTSFRAVQCQSRTPWRNVKHVKVTRY 188

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G  +   + + L  +DR      A  EGLY
Sbjct: 189 GEYIVVDIKANAFVHHMVRNIVGSLMEIGCGNQSENWMAELLALKDRNLAAATARAEGLY 248

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 249 LVSVDY 254


>gi|308270748|emb|CBX27358.1| tRNA pseudouridine synthase A [uncultured Desulfobacterium sp.]
          Length = 246

 Score =  165 bits (418), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 95/248 (38%), Positives = 138/248 (55%), Gaps = 4/248 (1%)

Query: 1   MIR-YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           MI+ + + IEY+G+ + GWQRQ NG +IQG IEKAIF +T + + + GAGRTD+GVHAL 
Sbjct: 1   MIKNFKLTIEYDGTAFNGWQRQLNGRTIQGEIEKAIFAMTKQKIALTGAGRTDAGVHALA 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F       P    + LN+ L   D I  L   + +K FH+R+ +  + Y Y+I+ R
Sbjct: 61  QVANFICDTNLEPDSFYRGLNSLLP-GDIIIKLCEQVCEK-FHSRYDSKSKLYRYKILNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD-VN 178
             P A+ +   W I   LD + MR A   + G  DF  F        S IRT+   + + 
Sbjct: 119 PLPSAIGRNYLWFIKSPLDLKAMREAVLFIAGTRDFKAFEGSGSPRKSTIRTVLRSELIE 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           +  N+I+  + A  FL   +R+ VGSL  VG GK    D++  L ++DR++    APP G
Sbjct: 179 NEDNIIQFEIEADGFLRFMVRNIVGSLISVGLGKLKPLDIKTILDSKDRRKASATAPPGG 238

Query: 239 LYFDSVEY 246
           L+   V Y
Sbjct: 239 LFLVKVRY 246


>gi|209518943|ref|ZP_03267753.1| tRNA pseudouridine synthase A [Burkholderia sp. H160]
 gi|209500595|gb|EEA00641.1| tRNA pseudouridine synthase A [Burkholderia sp. H160]
          Length = 270

 Score =  165 bits (418), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 131/246 (53%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + ++Y+G+ + GWQ Q +G+++Q  +E+A+   T   V    AGRTD GVH L Q
Sbjct: 1   MTRIALGVQYDGAAFAGWQSQPHGNTVQDELERALREFTRTPVQTVVAGRTDRGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   + V +   +  NA+L    TI +     +   FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELDRVDISWVRGPNAFLP--KTIGVQWAKPMPDDFHARFSAFERTYYYVLYVSP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   RA  +   LD + MR+AA+HL+G HDF+ FRS  CQ+ +P + +   DV   
Sbjct: 119 VRSPMLTTRAGWVHTPLDVDAMRLAAEHLIGEHDFSAFRSSQCQSKTPFKHLYQIDVKRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN +  R  A +FLH  +R+ +G L  +G G+  +  +   L ++ R    P   P+GLY
Sbjct: 179 GNFVHFRFRANAFLHHMVRNVMGCLIEIGSGRRPAAWMADVLASRSRDCAAPTFMPDGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAQVGY 244


>gi|86148380|ref|ZP_01066673.1| tRNA pseudouridine synthase A [Vibrio sp. MED222]
 gi|218708902|ref|YP_002416523.1| tRNA pseudouridine synthase A [Vibrio splendidus LGP32]
 gi|254764875|sp|B7VL84|TRUA_VIBSL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|85833863|gb|EAQ52028.1| tRNA pseudouridine synthase A [Vibrio sp. MED222]
 gi|218321921|emb|CAV17914.1| tRNA pseudouridine synthase A [Vibrio splendidus LGP32]
          Length = 264

 Score =  165 bits (418), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 137/246 (55%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG+ YFGWQRQ++  S+Q  +EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MKIALGIEYNGTHYFGWQRQRDVKSVQEELEKALSVVANHPVEVMCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +   V      NA   +   I++   + V++ FHARFSA  R Y Y I     
Sbjct: 61  VHFETNVDRKMVAWTMGANA--NMPKDIAVRWATEVNEDFHARFSATARRYRYIIFNHAL 118

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD + M  A Q+L+G +DFT+FR+ HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGHLDEKKMHEAGQYLLGENDFTSFRATHCQSRSPWRNMIHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I I + A +F+H  +R+  GSL  VG G      ++  L+A+DRK  G  A  EGLY
Sbjct: 178 GHYIVIDIKANAFVHHMVRNITGSLIAVGKGDQKPEWIQWLLEAKDRKVAGATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVDVDY 243


>gi|332992505|gb|AEF02560.1| tRNA pseudouridine synthase A [Alteromonas sp. SN2]
          Length = 263

 Score =  165 bits (418), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 97/247 (39%), Positives = 134/247 (54%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + IEY+G+   GWQRQK+ +S+Q  +EKA+ ++  + ++V  AGRTD+GVHA  Q
Sbjct: 1   MGRIALGIEYDGASVHGWQRQKDVASVQEYLEKALTVIANKPIIVFCAGRTDAGVHATGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII-TR 119
           + HFD   E         +NA   + DTI++     V   FHARFSA  R Y Y I  +R
Sbjct: 61  IVHFDSDVERPERAWTLGINA--NMPDTIAVTWAKPVSDDFHARFSATHRRYRYVIYNSR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L  G      + LD E M  AAQ LVG HDFTTFR+  CQ+ +P RT+    V+ 
Sbjct: 119 MRPAILHNGVTHEY-RELDAEKMHEAAQALVGEHDFTTFRASLCQSKTPHRTVSSVSVHR 177

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A +FLH  +R+  GSL  +G G+     +   L  +DR +    A P GL
Sbjct: 178 QGRYVVLDIRANAFLHHMVRNITGSLLCIGAGEQPVDWMAHLLTLKDRAKAATTAKPNGL 237

Query: 240 YFDSVEY 246
           Y   V Y
Sbjct: 238 YLVDVTY 244


>gi|307544826|ref|YP_003897305.1| tRNA pseudouridine synthase A [Halomonas elongata DSM 2581]
 gi|307216850|emb|CBV42120.1| tRNA pseudouridine synthase A [Halomonas elongata DSM 2581]
          Length = 292

 Score =  165 bits (418), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 93/241 (38%), Positives = 134/241 (55%), Gaps = 12/241 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M +EY+GS Y GWQR K+ +S+Q S+E+A+  V G  V VH +GRTDSGVHA RQ+ HFD
Sbjct: 1   MAVEYDGSQYCGWQRLKHAASVQASLEQALSRVAGAPVRVHASGRTDSGVHATRQIVHFD 60

Query: 66  LV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
                  + WV         A   +   I++  +  V + FHARF A+ R Y Y ++ + 
Sbjct: 61  PPAPRSEKAWV-------FGANANLPRDIAVRWVMPVGEDFHARFKALARRYRYVLLNQP 113

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +   LE+         LD E M  AAQ LVG HDF++FR+  CQ+ +P R +   +V+  
Sbjct: 114 SRPVLERANVTWCRDPLDAEAMHEAAQVLVGEHDFSSFRAAGCQSKTPWRHLHFIEVHRH 173

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G L+ + V   +FLH  IR+  G+L  VG G+  +  L + L  +DR +    AP  GL+
Sbjct: 174 GPLVVVDVQGNAFLHHMIRNIAGALVTVGRGEQGADYLARLLALRDRTQGDVTAPACGLH 233

Query: 241 F 241
           F
Sbjct: 234 F 234


>gi|91792843|ref|YP_562494.1| tRNA pseudouridine synthase A [Shewanella denitrificans OS217]
 gi|123061034|sp|Q12P55|TRUA_SHEDO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91714845|gb|ABE54771.1| tRNA pseudouridine synthase A [Shewanella denitrificans OS217]
          Length = 261

 Score =  165 bits (417), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 95/245 (38%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS Y GWQRQ    S+Q  +EKA+ L+  E + V  AGRTD+GVH   QV
Sbjct: 1   MRVALGIEYDGSSYCGWQRQVEVDSVQAQLEKALSLIANEPIEVVCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +NA L   DTI++  + +VD  FHARFSA  R Y Y I   + 
Sbjct: 61  VHFDTTVIRPDSAWTLGVNANL--PDTIAVRWVKLVDDSFHARFSATARRYRYVIYNHKF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L +         +D   M  AAQ L+G HDFT+FR++ CQ+ SP R++   +V   G
Sbjct: 119 RPGLLRHGLSHYHGDIDETLMHQAAQQLLGEHDFTSFRAMQCQSKSPFRSVHEVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+ VGSL  +G G      + K +  +DR++    A P GLY 
Sbjct: 179 MYIMVDIKANAFLHHMVRNIVGSLLEIGLGNQPLNWISKLIAVKDRRQAAATAKPNGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|261340711|ref|ZP_05968569.1| tRNA pseudouridine synthase A [Enterobacter cancerogenus ATCC
           35316]
 gi|288317127|gb|EFC56065.1| tRNA pseudouridine synthase A [Enterobacter cancerogenus ATCC
           35316]
          Length = 270

 Score =  165 bits (417), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 96/245 (39%), Positives = 135/245 (55%), Gaps = 4/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV 
Sbjct: 11  RIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVLCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQA 121
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   R  
Sbjct: 71  HFETTAVRKDAAWTLGVNANL--PGDIAVRWVKNVPDDFHARFSATARRYRYVIYNQRLR 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P  L +G      + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +G
Sbjct: 129 PAVLSQGVTHFY-EPLDAERMQRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVSRYG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY 
Sbjct: 188 AYVVVDIKANAFVHHMVRNIVGSLMEVGAGHQPESWIAELLAAKDRTLAAATAKAEGLYL 247

Query: 242 DSVEY 246
            SV+Y
Sbjct: 248 VSVDY 252


>gi|254670107|emb|CBA05050.1| tRNA pseudouridine synthase A [Neisseria meningitidis alpha153]
 gi|319409652|emb|CBY89952.1| tRNA pseudouridine synthase A (tRNA-uridine isomerase I; tRNA
           pseudouridylate synthase I) [Neisseria meningitidis WUE
           2594]
 gi|325201326|gb|ADY96780.1| tRNA pseudouridine synthase A [Neisseria meningitidis M01-240149]
 gi|325208888|gb|ADZ04340.1| tRNA pseudouridine synthase A [Neisseria meningitidis NZ-05/33]
          Length = 265

 Score =  165 bits (417), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 135/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQTALETALAQIAGEFVATTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAVRPQQAWVRGVNAHL--PEGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|229095128|ref|ZP_04226123.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock3-29]
 gi|228688313|gb|EEL42196.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock3-29]
          Length = 245

 Score =  165 bits (417), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MHNYKLTIQYDGARYKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI ++  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFKSDEKLVEHKVKKYLNQYL--PNDISITSVEEVPDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ E+M+ AA+HLVG HDFT F +   +  S +R +   +V+ 
Sbjct: 119 EHTNPFMRKHSMHVNKKLNVESMKKAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLEVSE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y +SVE+
Sbjct: 239 YLESVEF 245


>gi|293610220|ref|ZP_06692521.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827452|gb|EFF85816.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 265

 Score =  165 bits (417), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 93/248 (37%), Positives = 134/248 (54%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE+ +  +  E +V+HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKIADEPIVLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD           +  N+  ++   ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTNAIRPETGWLRGANS--QLPKDISIQWIKLMDENFHARFKATARRYRYIIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H  +  
Sbjct: 119 PHRPALLHKQVTYIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKHCRLFE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ VG L  +G G +    ++    AQDRK  G  APP+GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIVGCLLEIGQGMYEIDHIDAMFAAQDRKAAGVTAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIHCNYP 246


>gi|33152228|ref|NP_873581.1| tRNA pseudouridine synthase A [Haemophilus ducreyi 35000HP]
 gi|42559759|sp|Q7U335|TRUA_HAEDU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33148450|gb|AAP95970.1| tRNA pseudouridine synthase A [Haemophilus ducreyi 35000HP]
          Length = 261

 Score =  165 bits (417), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 98/247 (39%), Positives = 140/247 (56%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q ++E+A+  VT   + V  AGRTDSGVH   QV
Sbjct: 1   MKVALGIEYDGSNYFGWQRQAEVVSVQQTLEEALSKVTNTTIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E      C   NA+L  ++ I++     V + FHARFSA  R Y Y I   + 
Sbjct: 61  VHFDTEVERPLASWCFGTNAHL--ANDIAVKWAVKVAEDFHARFSATARRYRYIIFNSKL 118

Query: 122 PLA-LEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             A L KG A +  P  LD + M  A Q+L+G  DF++FR+  CQ+ +P R I H +V  
Sbjct: 119 RTAILPKGVAHYHYP--LDAQKMHQAGQYLLGEQDFSSFRAAKCQSHTPWRNIHHLNVVR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN + + + A +F+H  +R+ VGSL  VG G+     ++  L+ ++R+   P    EGL
Sbjct: 177 QGNYVIVDIQANAFVHHMVRNIVGSLLEVGQGRQPIEWIKWLLEQKNRQLAAPTTKAEGL 236

Query: 240 YFDSVEY 246
           Y  +VEY
Sbjct: 237 YLVNVEY 243


>gi|302770785|ref|XP_002968811.1| hypothetical protein SELMODRAFT_231248 [Selaginella moellendorffii]
 gi|300163316|gb|EFJ29927.1| hypothetical protein SELMODRAFT_231248 [Selaginella moellendorffii]
          Length = 300

 Score =  165 bits (417), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 101/277 (36%), Positives = 149/277 (53%), Gaps = 33/277 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           RY + IEY G+ + GWQRQ    ++QG++E A     G+ V   G+ RTD+GVHALR V 
Sbjct: 8   RYLVGIEYIGTRFSGWQRQGGVRTVQGTLEDAFSSFMGQSVSTTGSSRTDAGVHALRNVF 67

Query: 63  HFDLVR-----------EWVPVILCKALNAYL-KISDTISILNLSIVDKQFHARFSAIRR 110
           H DL R              P ++ +A+N +L + S  + +++   V   FHARF A  R
Sbjct: 68  HVDLARTSKRKPGELLAPHPPDVIVRAVNHFLQRESADVQVVDARFVPPDFHARFRAKER 127

Query: 111 SYLYRIITRQAPLAL-EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
           +Y YRI+      +L E+ RAW + + L+   M+ A Q L+G HDF++FR+  CQA+SPI
Sbjct: 128 TYYYRILAGSCRASLFERDRAWHVEEPLNLIAMQSACQVLLGTHDFSSFRASGCQAASPI 187

Query: 170 RTIDHFDV------------------NSFGNLIEIRVVAR--SFLHTQIRSFVGSLKLVG 209
           +T++   +                  +S  +L    V AR  SFL+ Q+R  VG+LK VG
Sbjct: 188 KTLEELSIRETVSWPHFLTGCSSNAQSSNPDLKSYVVTARAQSFLYHQVRLMVGTLKGVG 247

Query: 210 DGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            GK T  D+ K L+ +      P+AP  GL+   V+Y
Sbjct: 248 AGKRTVEDVRKILEGRSISLALPMAPASGLFLADVKY 284


>gi|153826201|ref|ZP_01978868.1| tRNA pseudouridine synthase A [Vibrio cholerae MZO-2]
 gi|149740061|gb|EDM54230.1| tRNA pseudouridine synthase A [Vibrio cholerae MZO-2]
          Length = 264

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHDELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL +VG G+     ++  L  +DR      A  EGLY
Sbjct: 178 GRYVVIDIKANAFVHHMVRNITGSLIVVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 238 LVSVDY 243


>gi|304315974|ref|YP_003851119.1| tRNA pseudouridine synthase A [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302777476|gb|ADL68035.1| tRNA pseudouridine synthase A [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 248

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 136/246 (55%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M    ++IEY+G+ Y GWQ QKN  +IQ +I KAI  +T E V + G+ RTD+GVHAL Q
Sbjct: 5   MRNIVLVIEYDGTNYHGWQIQKNVVTIQETITKAIKKITNEDVDLIGSSRTDAGVHALHQ 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F          +  ALN+ L     I I +    D  FH+R+SA  + Y Y I  R+
Sbjct: 65  VANFKTCTNIPTSKIPNALNSVLPAD--IVIKDAFEADMDFHSRYSAKGKRYKYIIYNRR 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               + K  +W I KSLD E MR + ++L G HDF+ F++      SP+RT+    +   
Sbjct: 123 FSSPILKNYSWHISKSLDVEKMRESLKYLEGTHDFSAFKASGSSVKSPVRTVRDISLKKN 182

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +E  + A  FL+  +R  VG++  VG GK    D+++ L +++R   G  APP+GL+
Sbjct: 183 GFNVEFEIEADGFLYNMVRIIVGTIVDVGLGKINPIDVKEILDSKNRCMAGKTAPPQGLF 242

Query: 241 FDSVEY 246
              + Y
Sbjct: 243 LTKIYY 248


>gi|228937724|ref|ZP_04100358.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228970604|ref|ZP_04131252.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977183|ref|ZP_04137582.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis Bt407]
 gi|228782492|gb|EEM30671.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis Bt407]
 gi|228789070|gb|EEM37001.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228821932|gb|EEM67926.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 250

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVYDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ E+M+ AA+HL G HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVESMKAAAKHLAGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPQILEAKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|325129355|gb|EGC52190.1| tRNA pseudouridine synthase A [Neisseria meningitidis OX99.30304]
          Length = 265

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALENALAQIAGEAVSTIVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESVPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSS 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|318606505|emb|CBY28003.1| tRNA pseudouridine synthase A [Yersinia enterocolitica subsp.
           palearctica Y11]
          Length = 280

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 101/246 (41%), Positives = 135/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           I+  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 19  IKIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVLCAGRTDAGVHATGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF    E         +N++L     I++  +  VD  FHARFSA  R Y Y I   R 
Sbjct: 79  VHFITTAERKNAAWTMGVNSHL--PPDIAVRWVKTVDDGFHARFSATARRYRYIIFNHRY 136

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD E M  AAQ L+G HDFT+FR+I CQ+ +P R + H  V   
Sbjct: 137 RPAVLAQGVTHCY-MPLDAEKMEQAAQCLLGEHDFTSFRAIQCQSRTPWRNVKHVKVTRH 195

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G  + T + + L  +DR      A  EGLY
Sbjct: 196 GAYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQSVTWMAELLALKDRARAAATAKAEGLY 255

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 256 LVSVDY 261


>gi|91777254|ref|YP_552462.1| tRNA pseudouridine synthase A [Burkholderia xenovorans LB400]
 gi|123167830|sp|Q13S27|TRUA_BURXL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91689914|gb|ABE33112.1| tRNA pseudouridine synthase [Burkholderia xenovorans LB400]
          Length = 270

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + ++Y+GS + GWQ Q +G+++Q  +E+A+       V    AGRTD+GVH L Q
Sbjct: 1   MKRIALGVQYDGSVFCGWQSQPHGNTVQDELERALREFAQTPVQTIVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +   V   +  N++L    TIS+     +  +FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELDRADVSWVRGTNSFLP--KTISVQWAKPMPDEFHARFSAFERTYYYVLYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   RA  +  +LD + M+ AA HL+G HDF+ FRS  CQ+ +P++ +   DV   
Sbjct: 119 VRSPMLAARAGWVHAALDVDAMQAAAAHLIGEHDFSAFRSSQCQSKTPVKHLYQIDVRQQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I  R  A +FLH  +R+ +G L  +G G+     + + L ++DR+   P   P+GLY
Sbjct: 179 GDFIHFRFRANAFLHHMVRNLMGCLVYIGRGRRPVEWMAEVLASRDREFAAPTFMPDGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAQVGY 244


>gi|332162419|ref|YP_004298996.1| tRNA pseudouridine synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325666649|gb|ADZ43293.1| tRNA pseudouridine synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330861403|emb|CBX71633.1| tRNA pseudouridine synthase A [Yersinia enterocolitica W22703]
          Length = 280

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 101/246 (41%), Positives = 135/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           I+  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 19  IKIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVLCAGRTDAGVHATGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF    E         +N++L     I++  +  VD  FHARFSA  R Y Y I   R 
Sbjct: 79  VHFITTAERKNAAWTMGVNSHL--PPDIAVRWVKTVDDGFHARFSATARRYRYIIFNHRY 136

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD E M  AAQ L+G HDFT+FR+I CQ+ +P R + H  V   
Sbjct: 137 RPAVLAQGVTHCY-MPLDAEKMEQAAQCLLGEHDFTSFRAIQCQSRTPWRNVKHVKVTRH 195

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G  + T + + L  +DR      A  EGLY
Sbjct: 196 GAYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQSVTWMAELLALKDRARAAATAKAEGLY 255

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 256 LVSVDY 261


>gi|308390134|gb|ADO32454.1| tRNA pseudouridine synthase [Neisseria meningitidis alpha710]
 gi|325204986|gb|ADZ00440.1| tRNA pseudouridine synthase A [Neisseria meningitidis M01-240355]
          Length = 265

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALENALAQIAGESVATTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD V         + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTVAVRPQQAWVRGVNAHLP--EGIAVLHAQQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIGPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|261496287|ref|ZP_05992691.1| tRNA-pseudouridine synthase I [Mannheimia haemolytica serotype A2
           str. OVINE]
 gi|261308049|gb|EEY09348.1| tRNA-pseudouridine synthase I [Mannheimia haemolytica serotype A2
           str. OVINE]
          Length = 279

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 94/252 (37%), Positives = 141/252 (55%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ+   S+Q  +E+A+ +V    V V  AGRTD+GVH   QV
Sbjct: 19  MKIALGIEYDGSRYFGWQRQEAVESVQQQLEQALSVVANSPVEVFCAGRTDAGVHGTGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA+L   D I++     V++ FHARFSA  R Y Y I     
Sbjct: 79  VHFETQANRPLQSWCFGTNAHL--PDDIAVKWAVAVNEDFHARFSATARRYRYIIFN--- 133

Query: 122 PLALEKGRAWLIPKS-------LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
               +K R+ ++PK        LD   M  A Q+L+G +DF++FR+  CQ+++P R I H
Sbjct: 134 ----QKLRSAILPKGVTHFHFPLDERKMHQAGQYLLGENDFSSFRAAKCQSNTPWRNIHH 189

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V+  GN + + + A +F+H  +R+ VG+L  +G GK +    +  L+ +DR++  P A
Sbjct: 190 LNVSRQGNYVIVDIQANAFVHHMVRNIVGTLLEIGQGKQSVEWAKWVLEQRDREKAAPTA 249

Query: 235 PPEGLYFDSVEY 246
             EGLY   V Y
Sbjct: 250 KAEGLYLVEVHY 261


>gi|293395134|ref|ZP_06639420.1| tRNA pseudouridine synthase A [Serratia odorifera DSM 4582]
 gi|291422311|gb|EFE95554.1| tRNA pseudouridine synthase A [Serratia odorifera DSM 4582]
          Length = 270

 Score =  164 bits (416), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 138/247 (55%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +++  + IEY+GS Y+GWQRQ+  +S+QG +E+A+  V    VVV  AGRTD+GVHA  Q
Sbjct: 8   VLKIALGIEYDGSRYYGWQRQQEVASVQGCLEQALSKVADAPVVVFCAGRTDAGVHATGQ 67

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-R 119
           V HF+             +N +L     I++  +S V + FHARFSA  R Y Y I   R
Sbjct: 68  VVHFETTARRKDAAWTMGVNTHL--PPDIAVRWVSEVREDFHARFSATARRYRYLIFNHR 125

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L++G        LD + M+ AAQ L+G +DFT+FR++ CQ+ +P R + H  V  
Sbjct: 126 YRPAVLQQGMTHFY-HPLDADRMQRAAQALLGENDFTSFRAVQCQSRTPWRNVKHVKVTR 184

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I + + A +F+H  +R+ VGSL  +G G      + + L  +DR      A  +GL
Sbjct: 185 HGQYIVVDIKANAFVHHMVRNIVGSLMEIGCGNQDENWMAELLALKDRNLAAATAKADGL 244

Query: 240 YFDSVEY 246
           Y  +V+Y
Sbjct: 245 YLVAVDY 251


>gi|325124398|gb|ADY83921.1| tRNA-pseudouridine synthase I [Acinetobacter calcoaceticus PHEA-2]
          Length = 265

 Score =  164 bits (416), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 93/248 (37%), Positives = 134/248 (54%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKIADEPIALHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD           +  N+  ++   ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTNAIRPETGWLRGANS--QLPKDISIQWIKLMDENFHARFKATARRYRYIIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H  +  
Sbjct: 119 PHRPALLHKQVTHIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKHCRLFE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ VG L  +G G +    ++    AQDRK  G  APP+GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIVGCLLEIGQGMYEIDHIDAMFAAQDRKAAGVTAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    YS
Sbjct: 239 YFIQCNYS 246


>gi|228983685|ref|ZP_04143885.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228776037|gb|EEM24403.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 250

 Score =  164 bits (416), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+   + G  RTD+GVHAL 
Sbjct: 6   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKETEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPQILEAKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|229194805|ref|ZP_04321592.1| tRNA pseudouridine synthase A 2 [Bacillus cereus m1293]
 gi|228588653|gb|EEK46684.1| tRNA pseudouridine synthase A 2 [Bacillus cereus m1293]
          Length = 250

 Score =  164 bits (416), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYALDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+A+ R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPHILEAKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|152971246|ref|YP_001336355.1| tRNA pseudouridine synthase A [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|166228703|sp|A6TC04|TRUA_KLEP7 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|150956095|gb|ABR78125.1| tRNA pseudouridine synthase A [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
          Length = 270

 Score =  164 bits (416), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 133/240 (55%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETR 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKHVPADFHARFSATARRYRYVIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +G      + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  +G  + +
Sbjct: 134 QGVTHF-HQPLDAERMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRYGAYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  SV+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAGNQPESWMAELLAAKDRTLAAATAKAEGLYLVSVDY 252


>gi|261820765|ref|YP_003258871.1| tRNA pseudouridine synthase A [Pectobacterium wasabiae WPP163]
 gi|261604778|gb|ACX87264.1| tRNA pseudouridine synthase A [Pectobacterium wasabiae WPP163]
          Length = 283

 Score =  164 bits (416), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 135/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ + +S+Q  +EKA+  V  E + V  AGRTD+GVH   QV
Sbjct: 23  LKIALGIEYDGSQYYGWQRQNDVASVQACLEKALSKVADEPIEVFCAGRTDAGVHGTGQV 82

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF              +NA L     I++  +  VD+ FHARFSA  R Y Y I   R 
Sbjct: 83  VHFTTQAIRKDAAWTMGVNANLPPD--IAVRWVKTVDEDFHARFSATARRYRYVIYNHRY 140

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G        LD E M  A Q L+G +DFT+FR++ CQ+ +P R ++H  V   
Sbjct: 141 RPAVLSHGMTHFY-HPLDVERMERAGQCLLGENDFTSFRAVQCQSRTPWRNVNHLKVTRH 199

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I + + A +F+H  +R+ VGSL  VG G    + + + L A+DR   G  A  EGLY
Sbjct: 200 GDYIVVDIKANAFVHHMVRNIVGSLMDVGCGNRPESWIAELLVAKDRTLAGATARAEGLY 259

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 260 LVAVDY 265


>gi|206974202|ref|ZP_03235119.1| tRNA pseudouridine synthase A [Bacillus cereus H3081.97]
 gi|217958024|ref|YP_002336568.1| tRNA pseudouridine synthase A [Bacillus cereus AH187]
 gi|222094223|ref|YP_002528280.1| tRNA pseudouridine synthase a [Bacillus cereus Q1]
 gi|206747442|gb|EDZ58832.1| tRNA pseudouridine synthase A [Bacillus cereus H3081.97]
 gi|217065270|gb|ACJ79520.1| tRNA pseudouridine synthase A [Bacillus cereus AH187]
 gi|221238278|gb|ACM10988.1| tRNA-pseudouridylate synthase I (tRNA pseudouridine synthase A)
           [Bacillus cereus Q1]
          Length = 245

 Score =  164 bits (416), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+A+ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPHILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|254429312|ref|ZP_05043019.1| tRNA pseudouridine synthase A [Alcanivorax sp. DG881]
 gi|196195481|gb|EDX90440.1| tRNA pseudouridine synthase A [Alcanivorax sp. DG881]
          Length = 267

 Score =  164 bits (416), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 92/253 (36%), Positives = 136/253 (53%), Gaps = 13/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + IEY+G+ + GWQ Q+ G  ++Q  +E A+  V    V V  AGRTD+GVH   
Sbjct: 1   MTRIALGIEYDGTDFRGWQTQQPGVRTVQECLEAALSKVANHPVAVVCAGRTDAGVHGTG 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD      ++ W+       + A   +   +++   + VD  FHARFSA+ R Y Y
Sbjct: 61  QVVHFDSEAPREMKSWI-------MGANTNLPRDVTVRWATPVDDAFHARFSAVSRRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            I     P AL + +     + LD   MR AA +LVG HDFT +RS+HCQA SP++T+  
Sbjct: 114 VIYNHARPPALFRNQVTWNYRPLDVAAMREAAAYLVGEHDFTAYRSVHCQAKSPLKTMHS 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            ++   G ++ +   A +FL   +R+  G L  VG GK  +    + L+ +DR++    A
Sbjct: 174 LELYEHGKVLVLEAHANAFLMHMVRNIAGVLMSVGAGKRPAHWAREVLEGRDRRKGAATA 233

Query: 235 PPEGLYFDSVEYS 247
           PP GLY   +EY 
Sbjct: 234 PPFGLYLVDIEYP 246


>gi|229137290|ref|ZP_04265906.1| tRNA pseudouridine synthase A 2 [Bacillus cereus BDRD-ST26]
 gi|228646193|gb|EEL02411.1| tRNA pseudouridine synthase A 2 [Bacillus cereus BDRD-ST26]
          Length = 250

 Score =  164 bits (416), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+A+ R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPHILEAKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|229917326|ref|YP_002885972.1| tRNA pseudouridine synthase A [Exiguobacterium sp. AT1b]
 gi|259550390|sp|C4KZL4|TRUA_EXISA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|229468755|gb|ACQ70527.1| tRNA pseudouridine synthase A [Exiguobacterium sp. AT1b]
          Length = 246

 Score =  164 bits (416), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 131/247 (53%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y G+Q Q NG++IQ  IE  +  +    V +  +GRTD+ VHAL Q
Sbjct: 1   MRRIKLIVAYDGTHYAGYQVQPNGNTIQAEIESVLARMHRHPVKIIASGRTDARVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   E       KALNA L   D I +     +D  FHAR+ A R+ Y Y I  RQ
Sbjct: 61  VIHFDTTLEMPAERFVKALNAML--PDDILVKQAEEMDDTFHARYGAKRKEYRYHI--RQ 116

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
                 +  A  +   L  E MR A + L+G HDFT+F     +    +RTI   +V   
Sbjct: 117 TEDPFRRHYAATVTYKLSLEAMRQAMERLIGTHDFTSFSVTKAEVEDRVRTIYEAEVLEM 176

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I  R V   FL+ Q+R  VG++  VG GK+   D+ + L+A+DR+  G  APP GLY
Sbjct: 177 GDEIIFRFVGSGFLYNQVRIMVGTVIEVGRGKYQPADITQMLEAKDRRVAGITAPPHGLY 236

Query: 241 FDSVEYS 247
             +V Y 
Sbjct: 237 LWNVNYE 243


>gi|326938210|gb|AEA14106.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 245

 Score =  164 bits (416), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVYDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ E+M+ AA+HL G HDFT F +   +  S +R +   DV  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVESMKAAAKHLAGSHDFTAFSNAKSKKKSMVREVYTLDVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPQILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|120598385|ref|YP_962959.1| tRNA pseudouridine synthase A [Shewanella sp. W3-18-1]
 gi|166229838|sp|A1RIB0|TRUA_SHESW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120558478|gb|ABM24405.1| tRNA pseudouridine synthase A [Shewanella sp. W3-18-1]
          Length = 261

 Score =  164 bits (416), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GSGYFGWQRQ    S+QG +E+A+ +V  E + +  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSGYFGWQRQAEVDSVQGQLERALSIVANEPIGLFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +NA   + D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNAIRNEGAWTLGVNA--NLPDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +        ++D + M  AAQ L+G  DFT+FR++ CQ+ +P R +   +V   G
Sbjct: 119 RPGILRHGVSHYHGNIDADKMHQAAQVLLGEQDFTSFRAVQCQSKTPFRNVHSVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDIAANAFLHHMVRNIVGSLLEIGLGNQPLTWMGDLLALKDRNQAAATAKPHGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|325206941|gb|ADZ02394.1| tRNA pseudouridine synthase A [Neisseria meningitidis M04-240196]
          Length = 265

 Score =  164 bits (415), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTIVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTAAARPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESVPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA +L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAAYLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSS 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|123441645|ref|YP_001005630.1| tRNA pseudouridine synthase A [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122088606|emb|CAL11401.1| tRNA pseudouridine synthase A [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 280

 Score =  164 bits (415), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 101/246 (41%), Positives = 135/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           I+  + IEYNGS YFGWQRQ+  +S+Q  +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 19  IKIALGIEYNGSRYFGWQRQQEVASVQACLEAALSKVANEPIGVLCAGRTDAGVHATGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF    E         +N++L     I++  +  VD  FHARFSA  R Y Y I   R 
Sbjct: 79  VHFITTAERKDAAWTMGVNSHL--PPDIAVRWVKTVDDGFHARFSATARRYRYIIFNHRY 136

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD E M  AAQ L+G HDFT+FR+I CQ+ +P R + H  V   
Sbjct: 137 RPAVLAQGVTHCY-MPLDAEKMAQAAQCLLGEHDFTSFRAIQCQSRTPWRNVKHVKVTRH 195

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G  + T + + L  +DR      A  EGLY
Sbjct: 196 GAYIVVDIKANAFVHHMVRNIVGSLIEIGCGNQSVTWMAELLALKDRARAAATAKAEGLY 255

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 256 LVSVDY 261


>gi|320183774|gb|EFW58608.1| tRNA pseudouridine synthase A [Shigella flexneri CDC 796-83]
          Length = 270

 Score =  164 bits (415), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 131/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L   D I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PDDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|228919351|ref|ZP_04082720.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228840287|gb|EEM85559.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 250

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MYNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|302877741|ref|YP_003846305.1| tRNA pseudouridine synthase A [Gallionella capsiferriformans ES-2]
 gi|302580530|gb|ADL54541.1| tRNA pseudouridine synthase A [Gallionella capsiferriformans ES-2]
          Length = 255

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 90/250 (36%), Positives = 137/250 (54%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G  Y GWQ Q  G ++Q +++ A+  +    V V+ AGRTD+GVHAL QV
Sbjct: 1   MRIALGVEYDGKPYCGWQSQPGGRTVQDTLQSALSHIADAPVTVNAAGRTDTGVHALEQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      +  WV     + +NA L  S  + +     V  +FHARFSA  RSY Y +
Sbjct: 61  VHFETDANRPLSAWV-----RGVNAMLPPS--VVVRWAHPVPDEFHARFSAQGRSYRYLL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           I +    A+  G+A      LD   MR AA +L+G HDF+ FR+  CQA SP++ ++  D
Sbjct: 114 INKPVRSAIHAGKAGWFHLPLDIALMREAAGYLLGEHDFSAFRAAECQAKSPVKCMNKID 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G+++   + A +FLH  +R+ VG L  VG GK+    +   L ++ R    P   P
Sbjct: 174 IYLNGDVLVFDLEANAFLHHMVRNIVGCLVYVGKGKYPPAWMADLLASRTRHLAAPTFSP 233

Query: 237 EGLYFDSVEY 246
           +GLY   ++Y
Sbjct: 234 DGLYLRRIQY 243


>gi|194290207|ref|YP_002006114.1| tRNA pseudouridine synthase a [Cupriavidus taiwanensis LMG 19424]
 gi|238692732|sp|B3R117|TRUA_CUPTR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|193224042|emb|CAQ70051.1| tRNA pseudouridylate synthase I [Cupriavidus taiwanensis LMG 19424]
          Length = 272

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 97/253 (38%), Positives = 141/253 (55%), Gaps = 10/253 (3%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ + GWQ Q + +++Q  +E AI    G  ++   AGRTD+GVHAL Q
Sbjct: 1   MNRIALGLHYDGAAFSGWQSQPHRNTVQDHLEDAIERFAGVRLLTTVAGRTDAGVHALGQ 60

Query: 61  VAHFD--LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           V H D  LVRE  P    + +NA+L  S  I++     VD  FHARF A  R Y Y + T
Sbjct: 61  VIHLDTELVRE--PFSWVRGVNAFLPPS--IALQWALPVDVGFHARFLAYERMYYYALYT 116

Query: 119 RQAPLALEKGRA--WLIP--KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
               + +  GRA   ++P  + LD E MR AA HL+G HDF+ FR+  CQA SP++T+  
Sbjct: 117 GPHRVPMVHGRAGYQMLPPGQRLDVEAMRAAAAHLIGEHDFSAFRAAECQAKSPVKTMYD 176

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   GN + +R  A +FLH  +R+ +G L  VG  ++    + + L  +DRK   P  
Sbjct: 177 VTIRDDGNWVFLRFRASAFLHHMVRNLMGCLVAVGRRRYPPDWMAQVLAGRDRKLAAPTF 236

Query: 235 PPEGLYFDSVEYS 247
            P+GLY   V+Y 
Sbjct: 237 MPDGLYLVGVKYP 249


>gi|134293154|ref|YP_001116890.1| tRNA pseudouridine synthase A [Burkholderia vietnamiensis G4]
 gi|166228688|sp|A4JMC2|TRUA_BURVG RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|134136311|gb|ABO57425.1| tRNA pseudouridine synthase A [Burkholderia vietnamiensis G4]
          Length = 270

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 91/249 (36%), Positives = 134/249 (53%), Gaps = 10/249 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVV--HG--AGRTDSGVHA 57
           +R  + ++Y+G+ + GWQ Q +G ++Q ++E+A+    GE   V  H   AGRTD+GVH 
Sbjct: 1   MRIALGVQYDGAAFCGWQAQPHGKTVQDALERAL----GEFACVPLHTTVAGRTDTGVHG 56

Query: 58  LRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRII 117
           L QV HFD   +       +  NA+L    T+S+     +   FHARFSA  R+Y Y + 
Sbjct: 57  LGQVVHFDTALDRAEFSWVRGTNAFLP--PTVSVQWAKAMPDTFHARFSAFERTYYYALY 114

Query: 118 TRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
                  +  GRA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   DV
Sbjct: 115 VHPVRSPMLAGRAGWIHTPLDDDAMRAAAVHLIGEHDFSSFRSSECQSKTPVKHLYQIDV 174

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G+ I  R  A +FLH  +R+ +G L  VG G++ +  L   L  +DR    P    +
Sbjct: 175 RRSGHFIHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWLADVLAGRDRNLAAPTFMAD 234

Query: 238 GLYFDSVEY 246
           GLY   V Y
Sbjct: 235 GLYLAHVGY 243


>gi|261252353|ref|ZP_05944926.1| tRNA pseudouridine synthase A [Vibrio orientalis CIP 102891]
 gi|260935744|gb|EEX91733.1| tRNA pseudouridine synthase A [Vibrio orientalis CIP 102891]
          Length = 264

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 93/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ Y+GWQRQ+   S+Q  +E+A+ +V  + + V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTQYYGWQRQREVKSVQEKLERALSVVANQPIEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V      NA L   D I++     V ++FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTATRKMVAWTMGANANL--PDDIAVRWAKEVPEEFHARFSATARRYRYIIFNSAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  AAQ+L+G +DFT+FR+ HCQ+ SP R + H +V    
Sbjct: 119 RPGILSSGVSHYHGELDEKKMHQAAQYLLGENDFTSFRATHCQSRSPWRNMMHINVTRHN 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + I + A +F+H  +R+  GSL  VG G+     + + L  +DRK  G  A  EGLY 
Sbjct: 179 QYVVIDIKANAFVHHMVRNITGSLICVGRGEQQPEWIAELLAVKDRKLAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|254506845|ref|ZP_05118984.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus 16]
 gi|219550130|gb|EED27116.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus 16]
          Length = 264

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 135/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ Y+GWQRQ++  S+Q  +EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTQYYGWQRQQDVKSVQEELEKALSVVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V      NA L     I++     V ++FHARF+A  R Y Y I     
Sbjct: 61  VHFDTTASRKMVAWTMGANANL--PGDIAVRWAKEVPEEFHARFTATARRYRYIIFNSAL 118

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD + M +AAQ+L+G +DFT+FR+ HCQ+ SP R + H +V   
Sbjct: 119 RPGILSTGVS-HYHGELDEKKMHLAAQYLLGENDFTSFRATHCQSRSPWRNMMHINVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I + A +F+H  +R+  GSL  VG G+     ++  L A+DRK  G  A  EGLY
Sbjct: 178 NQYVVIDIKANAFVHHMVRNITGSLICVGRGEQEPEWIQWLLGAKDRKLAGATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVDVDY 243


>gi|229114082|ref|ZP_04243507.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock1-3]
 gi|228669352|gb|EEL24769.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock1-3]
          Length = 245

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MHNYKLTIQYDGARYKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI ++  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFKSDEKLVEHKVKKYLNQYL--PNDISITSVEEVPDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ E+M+ AA+HLVG HDFT F +   +  S +R +   +V+ 
Sbjct: 119 EHTNPFMRKHSMHVNKKLNVESMKKAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLEVSE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y +S+E+
Sbjct: 239 YLESIEF 245


>gi|322806167|emb|CBZ03735.1| tRNA pseudouridine synthase A [Clostridium botulinum H04402 065]
          Length = 246

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+TGE + +  +GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIASGRTDTGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTTFQGSTDEILSYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ +P++LD E M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKHSYHVPETLDIEAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +++  +   FLH  IR   G+L  VG     S D++  L+A+DR++ GP AP +GL
Sbjct: 179 KDGYVDLVYLGSGFLHKMIRILTGTLIEVGLHNLKSVDVKNILEAEDRRKAGPTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV+Y
Sbjct: 239 FMTSVDY 245


>gi|152974254|ref|YP_001373771.1| tRNA pseudouridine synthase A [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152023006|gb|ABS20776.1| tRNA pseudouridine synthase A [Bacillus cytotoxicus NVH 391-98]
          Length = 260

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G  + GWQR   N ++IQG IE  +  + G+ + + G  RTD+GVHAL 
Sbjct: 16  MNNYKLTIQYDGGRFKGWQRLGNNDNTIQGKIESVLSEMIGQEIEIIGCSRTDAGVHALN 75

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F +  + V   + K LN YL   + ISI  +  V ++FHAR+++  ++YLY+I   
Sbjct: 76  QVANFKVDEKLVETKVKKYLNQYL--PNDISITEVEQVPERFHARYNSKTKTYLYKIWNE 133

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  +PK L+ ENM+ AA + +G HDFT F +   +  S +R I   DV  
Sbjct: 134 EHTNPFMRKYSMHVPKKLNVENMKQAAHYFIGSHDFTAFSNAKSKKKSMVREIYVLDVFE 193

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I+IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 194 SEGFIQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPQILEAKQRNQINCLADANGL 253

Query: 240 YFDSVEY 246
           Y + V++
Sbjct: 254 YLEKVDF 260


>gi|296104004|ref|YP_003614150.1| tRNA pseudouridine synthase A [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295058463|gb|ADF63201.1| tRNA pseudouridine synthase A [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 270

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 96/240 (40%), Positives = 132/240 (55%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVLCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AVRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYVIYNQRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +G      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ FG  + +
Sbjct: 134 QGVTHFY-EPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVSRFGAYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  SV+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAGHQPESWIAELLAAKDRTLAAATAKAEGLYLVSVDY 252


>gi|118476179|ref|YP_893330.1| tRNA pseudouridine synthase A [Bacillus thuringiensis str. Al
           Hakam]
 gi|228925681|ref|ZP_04088768.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228931917|ref|ZP_04094811.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228944241|ref|ZP_04106617.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229089549|ref|ZP_04220816.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock3-42]
 gi|229120089|ref|ZP_04249341.1| tRNA pseudouridine synthase A 2 [Bacillus cereus 95/8201]
 gi|118415404|gb|ABK83823.1| tRNA pseudouridine synthase A [Bacillus thuringiensis str. Al
           Hakam]
 gi|228663327|gb|EEL18915.1| tRNA pseudouridine synthase A 2 [Bacillus cereus 95/8201]
 gi|228693765|gb|EEL47461.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock3-42]
 gi|228815392|gb|EEM61637.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228827702|gb|EEM73442.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228833956|gb|EEM79506.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 250

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 141/247 (57%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYSLEVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLAAEAIPQILEAKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|157371571|ref|YP_001479560.1| tRNA pseudouridine synthase A [Serratia proteamaculans 568]
 gi|157323335|gb|ABV42432.1| tRNA pseudouridine synthase A [Serratia proteamaculans 568]
          Length = 273

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 137/246 (55%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+  +S+Q  +E+A+  V    + V  AGRTD+GVHA  QV
Sbjct: 12  LKIALGIEYDGSQYYGWQRQQEVASVQACLEQALSKVADAPINVLCAGRTDAGVHATGQV 71

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF+   +         +N +L     I++  ++ V++ FHARFSA  R Y Y I   R 
Sbjct: 72  VHFETTAQRKDAAWTMGVNTHL--PPDIAVRWVTGVNEDFHARFSATARRYRYIIYNHRY 129

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L+KG        LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V  +
Sbjct: 130 RPAVLQKGMTHFY-HPLDAERMERAAQALLGENDFTSFRTVQCQSRTPWRNVKHVKVTRY 188

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +F+H  +R+ VGSL  +G G      + + L  +DR      A  +GLY
Sbjct: 189 GEYIVVDIKANAFVHHMVRNIVGSLMEIGCGNQDENWMAELLALKDRNLAAATARADGLY 248

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 249 LVSVDY 254


>gi|33596565|ref|NP_884208.1| tRNA pseudouridine synthase A [Bordetella parapertussis 12822]
 gi|33601118|ref|NP_888678.1| tRNA pseudouridine synthase A [Bordetella bronchiseptica RB50]
 gi|42559762|sp|Q7U376|TRUA_BORPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|42559763|sp|Q7U386|TRUA_BORBR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|33566334|emb|CAE37247.1| tRNA pseudouridine synthase A [Bordetella parapertussis]
 gi|33575553|emb|CAE32631.1| tRNA pseudouridine synthase A [Bordetella bronchiseptica RB50]
          Length = 270

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 93/248 (37%), Positives = 139/248 (56%), Gaps = 4/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +G ++Q  +E A+  F   G  V    AGRTD+GVHA 
Sbjct: 1   MSRIALGLAYDGSAWQGWQTQPHGVTVQDQVEAALASFAGGGGPVATVCAGRTDTGVHAA 60

Query: 59  RQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
            QV H D   +       + +NA+L  S  I +     V + FHARFSA  R+Y+Y +  
Sbjct: 61  MQVIHLDTDLQRRDESWVRGVNAFLPPS--IVVQWARPVSEAFHARFSARSRTYVYLLWR 118

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
            +   AL  GRA    + LD   MR AA+ L+G HDF++FRS  CQA  P+RT+   D++
Sbjct: 119 GRVRPALWAGRAGWAFQPLDVPAMRAAARTLLGEHDFSSFRSSQCQARHPVRTLHRLDID 178

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  +   + A +FLH  +R+ +G+L  VG G+ +   ++  L+A+DR+   P   P+G
Sbjct: 179 ERGAFLVFTLRANAFLHHMVRNLIGALLQVGQGRESVAWMDALLRARDRRLGAPTFMPDG 238

Query: 239 LYFDSVEY 246
           LY  ++EY
Sbjct: 239 LYLSAIEY 246


>gi|298370079|ref|ZP_06981395.1| tRNA pseudouridine synthase A [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298281539|gb|EFI23028.1| tRNA pseudouridine synthase A [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 275

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ +++ Y+GS +FGWQ+Q  G  ++Q  +E AI  + GE + V  AGRTD+GVHA+ QV
Sbjct: 14  RWILVLSYDGSRFFGWQKQAEGIPTVQAELESAISKIAGENISVTVAGRTDTGVHAVAQV 73

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD      P    + +NAYL   D +++L        FHARF A  R Y Y + +   
Sbjct: 74  VHFDTAVFRPPQAWVRGVNAYLP--DGVAVLCAQTTQPHFHARFDAFGRRYRYLLQSAPV 131

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L KGRA      L+ E MR AA  LVG HDF++FR+  CQA SP++TI   ++    
Sbjct: 132 RSPLMKGRAGWTHLPLNLERMRQAAALLVGEHDFSSFRAAECQAKSPVKTIYSTEIGGGA 191

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +   +   +FLH  +R+ +G+L  VG G+         ++ + R +  P    +GLY 
Sbjct: 192 EWLYFDIHGNAFLHHMVRNIMGALVYVGCGRLDVGQFADLIKERSRLKAPPTFMSDGLYL 251

Query: 242 DSVEY 246
             V+Y
Sbjct: 252 TGVDY 256


>gi|261493083|ref|ZP_05989622.1| tRNA-pseudouridine synthase I [Mannheimia haemolytica serotype A2
           str. BOVINE]
 gi|261311262|gb|EEY12426.1| tRNA-pseudouridine synthase I [Mannheimia haemolytica serotype A2
           str. BOVINE]
          Length = 279

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 94/252 (37%), Positives = 140/252 (55%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ+   S+Q  +E+A+ +V    V V  AGRTD+GVH   QV
Sbjct: 19  MKIALGIEYDGSRYFGWQRQEAVESVQQQLEQALSVVANSPVEVFCAGRTDAGVHGTGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA+L   D I++     V++ FHARFSA  R Y Y I     
Sbjct: 79  VHFETQANRPLQSWCFGTNAHL--PDDIAVKWAVAVNEDFHARFSATARRYRYIIFN--- 133

Query: 122 PLALEKGRAWLIPKS-------LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
               +K R+ ++PK        LD   M  A Q+L+G +DF++FR+  CQ+++P R I H
Sbjct: 134 ----QKLRSAILPKGVTHFHFPLDERKMHQAGQYLLGENDFSSFRAAKCQSNTPWRNIHH 189

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V+  GN + + + A +F+H  +R+ VG+L  +G GK      +  L+ +DR++  P A
Sbjct: 190 LNVSRQGNYVIVDIQANAFVHHMVRNIVGTLLEIGQGKQPVEWAKWVLEQRDREKAAPTA 249

Query: 235 PPEGLYFDSVEY 246
             EGLY   V Y
Sbjct: 250 KAEGLYLVEVHY 261


>gi|240948735|ref|ZP_04753107.1| tRNA pseudouridine synthase A [Actinobacillus minor NM305]
 gi|240296951|gb|EER47529.1| tRNA pseudouridine synthase A [Actinobacillus minor NM305]
          Length = 262

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 98/252 (38%), Positives = 136/252 (53%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ++  S+Q  +E+A+  V    V V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQESVESVQQKLEEALSTVANSPVEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA+L   D I++     V + FHARFSA  R Y Y I  R  
Sbjct: 61  VHFETDANRPLQAWCFGTNAHL--PDDIAVKWAVEVPEDFHARFSATARRYRYIIFNR-- 116

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
                K R+ ++PK        LD E M  A Q+L+G +DF++FR+  CQ+ +P R I H
Sbjct: 117 -----KLRSAILPKGVSHYHVDLDHEKMHEAGQYLLGENDFSSFRAAKCQSHTPWRNIHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V+  G  I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A
Sbjct: 172 LNVSRLGAYIIVDIQANAFVHHMVRNIVGSLIEVGQGNQPPEWIKWLLEQKDRTLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
             EGLY   V Y
Sbjct: 232 KAEGLYLVDVHY 243


>gi|168705501|ref|ZP_02737778.1| tRNA pseudouridine synthase A [Gemmata obscuriglobus UQM 2246]
          Length = 263

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 92/242 (38%), Positives = 135/242 (55%), Gaps = 3/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVV-VHGAGRTDSGVHALRQVAHF 64
           +II Y+G+ +FGWQ Q    ++Q ++EKAI  +T E  V ++ +GRTDSGVHA+ QVA+ 
Sbjct: 6   LIIRYDGTDFFGWQTQPGRRTVQETVEKAIAEITREPRVRLNCSGRTDSGVHAVGQVANV 65

Query: 65  DLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
               +    +L KA+NA  K+ + + +  ++   + F A   A+R+ Y Y +   +    
Sbjct: 66  YTASKLSCAVLLKAINA--KLPEDVGVREVTEAPQSFCANKDAVRKMYRYVVQDGRLQDP 123

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             +  AW + + L+ E M  A++ LVGRHDF  F +      + +RTI H  VN FG  I
Sbjct: 124 FLRKYAWFVRQHLNAEAMARASRCLVGRHDFRCFETEWPNRLTSVRTITHLSVNRFGECI 183

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I V A  FL+  +R+  GSL  VG G W  T +   L A DR+  GP APPEGL+   V
Sbjct: 184 WIDVEANGFLYNMVRAIAGSLVQVGRGFWPETQIADVLHAMDRRLAGPTAPPEGLFLMRV 243

Query: 245 EY 246
            Y
Sbjct: 244 TY 245


>gi|153813476|ref|ZP_01966144.1| hypothetical protein RUMOBE_03896 [Ruminococcus obeum ATCC 29174]
 gi|149830420|gb|EDM85512.1| hypothetical protein RUMOBE_03896 [Ruminococcus obeum ATCC 29174]
          Length = 250

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 134/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG +IQG +  A+  + GE + + GA RTD+GVHAL  
Sbjct: 5   MKRVGLVVAYDGTNYSGWQIQPNGITIQGVLNDALTDLLGEKIEIMGASRTDAGVHALGN 64

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  ALN   ++ + I I     V+  FH R+    ++Y YRI+ R+
Sbjct: 65  VAVFDTNTRIPGEKISYALNQ--RLPEDIRIQLSEEVEPDFHPRYCDSEKTYEYRILNRK 122

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  E+  ++     LD + MR A  +L+GRHDF +F     Q  S +RT+   D+   
Sbjct: 123 FPVPTERLYSYFYHYKLDVDKMREATSYLIGRHDFASFCGTGAQVKSTVRTLTGIDIWRD 182

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++ IRV    FL+  +R   G+L  VG+G++    ++K L A DR   GP AP  GL 
Sbjct: 183 GDIVTIRVKGEGFLYNMVRIIAGTLIQVGNGQYPPERVKKILDACDRSVSGPTAPAHGLT 242

Query: 241 FDSVEY 246
              +E+
Sbjct: 243 LMGIEF 248


>gi|119945656|ref|YP_943336.1| tRNA pseudouridine synthase A [Psychromonas ingrahamii 37]
 gi|166228751|sp|A1SW72|TRUA_PSYIN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119864260|gb|ABM03737.1| tRNA pseudouridine synthase A [Psychromonas ingrahamii 37]
          Length = 261

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 98/247 (39%), Positives = 138/247 (55%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQK   S+Q  +E+++  +    V VH AGRTDSGVH+  QV
Sbjct: 1   MRIALGIEYDGAAYYGWQRQKEVISVQQELEQSLSKIANHTVRVHCAGRTDSGVHSTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+       V     +NA L     I++  +  VD  FHARFSA  R Y Y II   A
Sbjct: 61  VHFETEAIRKDVAWTLGVNANL--PKDIAVRWVKQVDSSFHARFSATARHYRY-IIYNGA 117

Query: 122 --PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L  G +      LD + M +A Q L+G  DFT+FR++HCQASSP++ I++ +++ 
Sbjct: 118 FRPGILGTGLSHY-HMDLDVQKMHLAGQMLLGEQDFTSFRALHCQASSPVKCIEYLNISQ 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I I + A +FLH  +R+  GSL  +G GK     L+  L  +DR +    A P GL
Sbjct: 177 RSQFIIIDIKANAFLHHMVRNIAGSLIEIGCGKQPVDWLKTLLAYKDRSKAAATAKPGGL 236

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 237 YLVEVDY 243


>gi|47567253|ref|ZP_00237967.1| tRNA pseudouridine synthase A [Bacillus cereus G9241]
 gi|47556096|gb|EAL14433.1| tRNA pseudouridine synthase A [Bacillus cereus G9241]
          Length = 245

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+A+ R +   LA   GL
Sbjct: 179 EAGCVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPHILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|332307082|ref|YP_004434933.1| tRNA pseudouridine synthase A [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332174411|gb|AEE23665.1| tRNA pseudouridine synthase A [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 263

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 93/245 (37%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G+G+ GWQRQ    S+Q  +E+A+  +  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGVEYDGAGFHGWQRQNEVISVQQHLEEALTRIANEPIRVVCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +N YL   DT+S+  +  V   FHARFSA  R Y Y I     
Sbjct: 61  VHFETNSQRPDRAWTLGINTYL--PDTVSVRWVKAVPDDFHARFSATARRYRYIIYNSTL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +       I   LD E M  AAQ LVG+HDF++FR+++CQA +  RT+ H  V   G
Sbjct: 119 RSGILANGVTHIYGDLDHELMNQAAQKLVGKHDFSSFRAVNCQAKTATRTMSHIRVKRMG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I V A +FLH  +R+  G+L  +G  +     +++ L+ +DR + G  A P GLY 
Sbjct: 179 DYIVIDVQANAFLHHMVRNITGTLVAIGHKEKPVEWVDELLEVKDRTKAGITALPNGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VHVTY 243


>gi|206580474|ref|YP_002237289.1| tRNA pseudouridine synthase A [Klebsiella pneumoniae 342]
 gi|288934225|ref|YP_003438284.1| tRNA pseudouridine synthase A [Klebsiella variicola At-22]
 gi|290508428|ref|ZP_06547799.1| tRNA pseudouridine synthase A [Klebsiella sp. 1_1_55]
 gi|238057733|sp|B5XNR9|TRUA_KLEP3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|206569532|gb|ACI11308.1| tRNA pseudouridine synthase A [Klebsiella pneumoniae 342]
 gi|288888954|gb|ADC57272.1| tRNA pseudouridine synthase A [Klebsiella variicola At-22]
 gi|289777822|gb|EFD85819.1| tRNA pseudouridine synthase A [Klebsiella sp. 1_1_55]
          Length = 270

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 135/247 (54%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   Q
Sbjct: 9   IFKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQ 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-R 119
           V HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I   R
Sbjct: 69  VVHFETRAQRKDAAWTLGVNANL--PGDIAVRWVKHVPADFHARFSATARRYRYVIYNHR 126

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L  G      + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  
Sbjct: 127 LRPAVLSHGVTHF-HQPLDAERMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTR 185

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           +G  + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGL
Sbjct: 186 YGAYVVVDIKANAFVHHMVRNIVGSLMEVGAGNQPESWMAELLAAKDRTLAAATAKAEGL 245

Query: 240 YFDSVEY 246
           Y  SV+Y
Sbjct: 246 YLVSVDY 252


>gi|238895838|ref|YP_002920574.1| tRNA pseudouridine synthase A [Klebsiella pneumoniae NTUH-K2044]
 gi|329997357|ref|ZP_08302740.1| tRNA pseudouridine synthase A [Klebsiella sp. MS 92-3]
 gi|238548156|dbj|BAH64507.1| tRNA pseudouridine synthase A [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|328539106|gb|EGF65142.1| tRNA pseudouridine synthase A [Klebsiella sp. MS 92-3]
          Length = 270

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 132/240 (55%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETR 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKHVPADFHARFSATARRYRYVIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
            G      + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  +G  + +
Sbjct: 134 HGVTHF-HQPLDAERMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRYGAYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  SV+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAGNQPESWMAELLAAKDRTLAAATAKAEGLYLVSVDY 252


>gi|153816265|ref|ZP_01968933.1| hypothetical protein RUMTOR_02514 [Ruminococcus torques ATCC 27756]
 gi|317501758|ref|ZP_07959944.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088721|ref|ZP_08337631.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 3_1_46FAA]
 gi|145846448|gb|EDK23366.1| hypothetical protein RUMTOR_02514 [Ruminococcus torques ATCC 27756]
 gi|316896791|gb|EFV18876.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330407244|gb|EGG86747.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 3_1_46FAA]
          Length = 271

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 135/247 (54%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +++  + KA+  +T E V V GA RTD+GVHA   
Sbjct: 1   MRRIKLTVAYDGTDYCGWQIQPNGITVEEVLNKALSDLTKETVKVIGASRTDAGVHARGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P  +  A+NA L   D I ++    V   +H R+    ++Y Y I+ R+
Sbjct: 61  VAVFDTKSPIPPERIAYAVNALL--PDDIVVVRSEEVGCDWHPRYQNSIKTYEYTIVNRE 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +  +W +   LD ++M+ AA++ +G HDF TF S+H    + +R ID  DV   
Sbjct: 119 MPDPLRRRDSWFVSFPLDIDDMKKAARYFIGEHDFKTFCSVHTGVKTTVRRIDSLDVEKK 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I+IR+    FL+  +R   G+L  VG G +  +++++ L+ ++R   G  APP+GL 
Sbjct: 179 GERIKIRISGNGFLYNMVRIIAGTLVEVGRGAFAPSEVKEMLEQKERGRAGATAPPQGLV 238

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 239 LLGIVYD 245


>gi|313680524|ref|YP_004058263.1| tRNA pseudouridine synthase a [Oceanithermus profundus DSM 14977]
 gi|313153239|gb|ADR37090.1| tRNA pseudouridine synthase A [Oceanithermus profundus DSM 14977]
          Length = 251

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 93/249 (37%), Positives = 141/249 (56%), Gaps = 7/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  +++EY+G+ + G+Q Q  G  ++QG +E A+  + G    V  AGRTDSGVHAL 
Sbjct: 1   MRRLKLVLEYDGTDFAGFQLQARGERTVQGVLEAALARIPGARPKVTAAGRTDSGVHALA 60

Query: 60  QVAHFDLVREWVPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
              H+D   + VPV  + +ALNA L     + +L    V   +HAR+SA  R YLYR++ 
Sbjct: 61  MPVHYD-TEDTVPVERVPQALNALL--PPDVRVLEAEEVPPDWHARYSARWRRYLYRVLN 117

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R+ P AL++ R W +P+  D   +  AA+ LVG HDF  F +   +A+  +R +    V 
Sbjct: 118 RRQPTALDRHRVWWVPQPFDFPAIAAAARTLVGEHDFGAFANREKRAT--VRRLYQAHVE 175

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           + G  + +  V   F+  Q+R+ VG+L  VG G+    D+ + L+  +R E G  APP+G
Sbjct: 176 AVGGELHLHFVGSGFVRGQVRAMVGTLVEVGLGRRPPEDVARLLENPERSEGGATAPPQG 235

Query: 239 LYFDSVEYS 247
           LYF +  YS
Sbjct: 236 LYFVAAGYS 244


>gi|262043366|ref|ZP_06016493.1| tRNA pseudouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|259039278|gb|EEW40422.1| tRNA pseudouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
          Length = 270

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 132/240 (55%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETR 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKRVPADFHARFSATARRYRYVIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
            G      + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  +G  + +
Sbjct: 134 HGVTHF-HQPLDAERMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRYGAYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  SV+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAGNQPESWMAELLAAKDRTLAAATAKAEGLYLVSVDY 252


>gi|196034640|ref|ZP_03102048.1| tRNA pseudouridine synthase A [Bacillus cereus W]
 gi|196045298|ref|ZP_03112530.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB108]
 gi|218901631|ref|YP_002449465.1| tRNA pseudouridine synthase A [Bacillus cereus AH820]
 gi|300119051|ref|ZP_07056762.1| tRNA pseudouridine synthase A [Bacillus cereus SJ1]
 gi|301052143|ref|YP_003790354.1| tRNA pseudouridine synthase A [Bacillus anthracis CI]
 gi|195992683|gb|EDX56643.1| tRNA pseudouridine synthase A [Bacillus cereus W]
 gi|196023882|gb|EDX62557.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB108]
 gi|218540034|gb|ACK92432.1| tRNA pseudouridine synthase A [Bacillus cereus AH820]
 gi|298723667|gb|EFI64398.1| tRNA pseudouridine synthase A [Bacillus cereus SJ1]
 gi|300374312|gb|ADK03216.1| tRNA pseudouridine synthase A [Bacillus cereus biovar anthracis
           str. CI]
          Length = 245

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 141/247 (57%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYSLEVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLAAEAIPQILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|28898964|ref|NP_798569.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus RIMD
           2210633]
 gi|260365288|ref|ZP_05777845.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus K5030]
 gi|260878838|ref|ZP_05891193.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AN-5034]
 gi|260896240|ref|ZP_05904736.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus Peru-466]
 gi|260899991|ref|ZP_05908386.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ4037]
 gi|31340461|sp|Q87MP1|TRUA_VIBPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|28807183|dbj|BAC60453.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus RIMD
           2210633]
 gi|308088841|gb|EFO38536.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus Peru-466]
 gi|308094227|gb|EFO43922.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AN-5034]
 gi|308107376|gb|EFO44916.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus AQ4037]
 gi|308115414|gb|EFO52954.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus K5030]
 gi|328474496|gb|EGF45301.1| tRNA pseudouridine synthase A [Vibrio parahaemolyticus 10329]
          Length = 264

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 94/245 (38%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ YFGWQRQ+   S+Q  +EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTNYFGWQRQREVKSVQEELEKALSIVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V      NA   +   I++     V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNVNRKMVAWTMGANA--NMPSDIAVRWAKEVPDDFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q+L+G +DF++FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDEKKMHEAGQYLLGENDFSSFRAAHCQSLSPCRNLMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY 
Sbjct: 179 DYVVIDIKANAFVHHMVRNITGSLIKVGRGEEKPEWIKWLLEAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|311278721|ref|YP_003940952.1| tRNA pseudouridine synthase A [Enterobacter cloacae SCF1]
 gi|308747916|gb|ADO47668.1| tRNA pseudouridine synthase A [Enterobacter cloacae SCF1]
          Length = 270

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 96/240 (40%), Positives = 132/240 (55%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E V V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPVTVFCAGRTDAGVHGTGQVVHFETR 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            E         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AERKDAAWTLGVNANL--PGDIAVRWVKYVADDFHARFSATARRYRYVIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +G      + LD   M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V  +G  + +
Sbjct: 134 QGVT-HYHQPLDAARMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVERYGAYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  SV+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAGNQPESWIAELLAAKDRTLAAATAKAEGLYLVSVDY 252


>gi|238916297|ref|YP_002929814.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
 gi|238871657|gb|ACR71367.1| tRNA-pseudouridine synthase I [Eubacterium eligens ATCC 27750]
          Length = 253

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q    +I+  ++KAI  +TGE V V GA RTD+GVHA   
Sbjct: 1   MRRIKLIVAYDGTEYSGWQIQPEAPTIEMCLDKAIRELTGENVHVTGASRTDAGVHAYGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN +L   D+I I +   V   FH R    R++Y YRI+   
Sbjct: 61  VAVFDTESTIPGDRFTFALNRFL--PDSIVIQDSWEVSGDFHPRHCNTRKTYEYRILNTV 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            PL  ++   W +  S+D E M+ AA ++VG HDF +F  +  QA S +RTI   +V   
Sbjct: 119 VPLPQKRNFTWHVTGSIDIEKMKEAAAYIVGEHDFKSFCCVRTQAESTVRTIYSLEVLQE 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I IR+    FL+  +R   G+L  VG G++    +++ L+A+DR   G  APP+GL 
Sbjct: 179 GSEIIIRIKGNGFLYNMVRIITGTLIQVGKGRFKPEYVKQMLEAKDRTVAGQTAPPQGLT 238

Query: 241 FDSVEY 246
              +EY
Sbjct: 239 LVGIEY 244


>gi|113868577|ref|YP_727066.1| tRNA pseudouridine synthase A [Ralstonia eutropha H16]
 gi|123032833|sp|Q0K8H3|TRUA_RALEH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|113527353|emb|CAJ93698.1| transfer RNA-pseudouridine synthase I [Ralstonia eutropha H16]
          Length = 272

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 94/251 (37%), Positives = 140/251 (55%), Gaps = 6/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ + GWQ Q + +++Q  +E AI    G  ++   AGRTD+GVHAL Q
Sbjct: 1   MNRIALGLHYDGAAFSGWQSQPHRNTVQDHLENAIERFAGVRLLTTVAGRTDTGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D   E  P    + +NA+L  S  I++     VD+ FHARF A  R Y Y + T  
Sbjct: 61  VIHLDTALEREPFSWVRGVNAFLPPS--IALQWALPVDQGFHARFLAFERMYYYALYTGP 118

Query: 121 APLALEKGRA--WLIP--KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             + L  GRA   ++P  + LD + MR AA  L+G HDF+ FR+  CQA SP++T+    
Sbjct: 119 HRVPLVHGRAGYQMLPPGQRLDVDAMREAAACLLGEHDFSAFRAAECQAKSPVKTMYDVT 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   GN + +R  A +FLH  +R+ +G L  VG G++ +  L + L  ++RK   P   P
Sbjct: 179 IRDDGNWVFLRFRASAFLHHMVRNLMGCLVAVGRGRYPAHWLAQVLAGRERKLAAPTFMP 238

Query: 237 EGLYFDSVEYS 247
           +GLY   V+Y 
Sbjct: 239 DGLYLVGVKYP 249


>gi|332798239|ref|YP_004459738.1| tRNA pseudouridine synthase A [Tepidanaerobacter sp. Re1]
 gi|332695974|gb|AEE90431.1| tRNA pseudouridine synthase A [Tepidanaerobacter sp. Re1]
          Length = 243

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 91/242 (37%), Positives = 139/242 (57%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +++EY G+ Y GWQRQKN  SIQ  +E AI  +TGE V V G+GRTD+GVHAL QVA+F 
Sbjct: 5   ILLEYEGTAYSGWQRQKNAISIQEVLENAIKSITGEAVNVIGSGRTDAGVHALGQVANFK 64

Query: 66  LVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
             +  +P+  L  A+N+  K+ + I + +  IV + FHARF A  + Y Y I   + P  
Sbjct: 65  -TQTKIPIEKLPYAINS--KLPEDIVVKHAEIVPEDFHARFWAKAKIYTYTIYNAKFPSP 121

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L K  ++  P+ L+   M+ AA  L+G HDF +F + +    S +R I+  +V   G+++
Sbjct: 122 LLKRYSYFYPRPLNVRAMKKAADMLIGTHDFASFMASNSPVKSTVRCIERLEVFQNGDIV 181

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +  + A  FL+  +R   G+L  VG  K  + D+   ++++DR   G   PP+GL    V
Sbjct: 182 KFEIEANGFLYNMVRIIAGTLLDVGINKKKANDIISIIKSKDRSMAGKTLPPQGLCLIKV 241

Query: 245 EY 246
            Y
Sbjct: 242 IY 243


>gi|30018678|ref|NP_830309.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|206967868|ref|ZP_03228824.1| tRNA pseudouridine synthase A [Bacillus cereus AH1134]
 gi|218230891|ref|YP_002365270.1| tRNA pseudouridine synthase A [Bacillus cereus B4264]
 gi|229068175|ref|ZP_04201482.1| tRNA pseudouridine synthase A 2 [Bacillus cereus F65185]
 gi|229108094|ref|ZP_04237719.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock1-15]
 gi|229125922|ref|ZP_04254947.1| tRNA pseudouridine synthase A 2 [Bacillus cereus BDRD-Cer4]
 gi|296501252|ref|YP_003662952.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
 gi|42559783|sp|Q813Z9|TRUA2_BACCR RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|29894219|gb|AAP07510.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|206736788|gb|EDZ53935.1| tRNA pseudouridine synthase A [Bacillus cereus AH1134]
 gi|218158848|gb|ACK58840.1| tRNA pseudouridine synthase A [Bacillus cereus B4264]
 gi|228657580|gb|EEL13393.1| tRNA pseudouridine synthase A 2 [Bacillus cereus BDRD-Cer4]
 gi|228675369|gb|EEL30588.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock1-15]
 gi|228714989|gb|EEL66857.1| tRNA pseudouridine synthase A 2 [Bacillus cereus F65185]
 gi|296322304|gb|ADH05232.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
          Length = 245

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|152979369|ref|YP_001344998.1| tRNA pseudouridine synthase A [Actinobacillus succinogenes 130Z]
 gi|171704324|sp|A6VQ16|TRUA_ACTSZ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|150841092|gb|ABR75063.1| tRNA pseudouridine synthase A [Actinobacillus succinogenes 130Z]
          Length = 264

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 95/252 (37%), Positives = 135/252 (53%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EYNG  YFGWQRQ+   S+Q  +EKA+  V  E + +  AGRTDSGVH   QV
Sbjct: 1   MKIALGVEYNGKRYFGWQRQEKVLSVQEELEKALSFVANEKIDLFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   E V      A      + D I++      D +FHARFSA  R Y Y I T   
Sbjct: 61  VHFET--EVVRPERAWAFGTNANLPDDIAVKWAKTADDEFHARFSATARRYRYLIYTN-- 116

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           PL     R+ ++P+        LD E M  A Q L+G +DF++FR+  CQ+ +P R + H
Sbjct: 117 PL-----RSAVLPEGVTHCHLPLDHEKMHEAGQFLLGENDFSSFRAAQCQSKTPWRNVHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G  I + + A +F+H  +R+ VGSL  VG G+     ++  L+ ++RK   P A
Sbjct: 172 LQVTRHGRYIVVDIQANAFVHHMVRNIVGSLMEVGSGRQPVEWMKWLLEQRNRKLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
            P+GLY   V Y
Sbjct: 232 KPQGLYLVRVTY 243


>gi|146312509|ref|YP_001177583.1| tRNA pseudouridine synthase A [Enterobacter sp. 638]
 gi|166991163|sp|A4WCV2|TRUA_ENT38 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145319385|gb|ABP61532.1| tRNA pseudouridine synthase A [Enterobacter sp. 638]
          Length = 270

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 95/245 (38%), Positives = 135/245 (55%), Gaps = 4/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  + + V  AGRTD+GVH   QV 
Sbjct: 11  RIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANQPIAVCCAGRTDAGVHGTGQVV 70

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQA 121
           HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   R  
Sbjct: 71  HFETTSVRKDAAWTLGVNANL--PGDIAVRWVKDVPDDFHARFSATARRYRYIIYNQRLR 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
           P  L +G      + LD E M+ AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +G
Sbjct: 129 PAVLGQGVTHFY-EPLDAERMQRAAQSLIGENDFTSFRAVQCQSRTPWRNVMHINVSRYG 187

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY 
Sbjct: 188 AYVVVDIKANAFVHHMVRNIVGSLMEVGAGHQPESWIAELLAAKDRTLAAATAKAEGLYL 247

Query: 242 DSVEY 246
            SV+Y
Sbjct: 248 VSVDY 252


>gi|117619854|ref|YP_857188.1| tRNA pseudouridine synthase A [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|166228676|sp|A0KLN7|TRUA_AERHH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|117561261|gb|ABK38209.1| tRNA pseudouridine synthase A [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 269

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 95/245 (38%), Positives = 133/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ+   S+Q  +EKA+  +    V +  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSRYFGWQRQREVISVQEELEKALSRIANHPVSIQCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             LN+ L     I++  +  VD+ FHARFSA  R Y Y I     
Sbjct: 61  IHFDTDANRAEGAWTLGLNSNLP--PDIAVRWVKQVDEGFHARFSATARRYRYVIYNHNY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+         +++D + M  A Q L+G HDF+TFR++ CQ+++P R + H  V+  G
Sbjct: 119 RPAILGSGVSHYHETIDADLMHQAGQSLLGEHDFSTFRAVACQSNTPWRNVTHLCVSRSG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+  GSL LVG G      + + L A+DR   GP A   GLY 
Sbjct: 179 PYIVLDIKANAFLHHMVRNITGSLLLVGQGLQPVEWIAEVLAARDRNLAGPTAKAGGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|210618029|ref|ZP_03291864.1| hypothetical protein CLONEX_04097 [Clostridium nexile DSM 1787]
 gi|210149022|gb|EEA80031.1| hypothetical protein CLONEX_04097 [Clostridium nexile DSM 1787]
          Length = 245

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 133/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I Y+G+ Y GWQ Q NG +++  + KA+  +TGE + V GA RTDSGVHAL  
Sbjct: 1   MKRIKLTIAYDGTNYCGWQVQPNGITVEEVVNKALKKLTGEDIQVIGASRTDSGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P  +  ALN   ++ + I I+    V + FH R+    ++Y Y I+  +
Sbjct: 61  VAVFDTHTTIPPERISYALNQ--RLPEDIVIVKSEEVAEDFHPRYCDCSKTYEYHILNMR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  ++   + +   LD E MR AA +L+G HDF +F ++       +RT+   ++   
Sbjct: 119 IPIPTKRLTNYFVSYDLDVEKMRKAAGYLIGEHDFVSFCNVRTDVEDTVRTVTELEILKD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I IR+    FL+  +R  VG+L  VG G +    +++ L+A+DRK  G  APP GL 
Sbjct: 179 GEEITIRISGNGFLYNMVRIIVGTLIRVGRGFYEPEKVKEILEAKDRKAAGVTAPPHGLI 238

Query: 241 FDSVEYS 247
              + Y 
Sbjct: 239 LAEIRYE 245


>gi|163801903|ref|ZP_02195800.1| tRNA pseudouridine synthase A [Vibrio sp. AND4]
 gi|159174411|gb|EDP59215.1| tRNA pseudouridine synthase A [Vibrio sp. AND4]
          Length = 264

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 94/245 (38%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEYNG+ YFGWQRQ+   S+Q  +EKA+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYNGTNYFGWQRQREVKSVQQELEKALSVVANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V      NA   +   I++     V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNVSRKMVAWTMGANA--NMPSDIAVRWAVEVSDDFHARFSATARRYRYIIFNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           LD + M  A Q+L+G +DF++FR+ HCQ+ SP R + H +V   G
Sbjct: 119 RPGILNSGVSHYHGELDEKKMHEAGQYLLGENDFSSFRAAHCQSLSPCRNMMHLNVTRHG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  VG G+     ++  L A+DRK  G  A  EGLY 
Sbjct: 179 DYVVIDIKANAFVHHMVRNITGSLIKVGRGEEKPAWIKSLLDAKDRKLAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|15641014|ref|NP_230645.1| tRNA pseudouridine synthase A [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121587328|ref|ZP_01677099.1| tRNA pseudouridine synthase A [Vibrio cholerae 2740-80]
 gi|147674772|ref|YP_001216471.1| tRNA pseudouridine synthase A [Vibrio cholerae O395]
 gi|153819838|ref|ZP_01972505.1| tRNA pseudouridine synthase A [Vibrio cholerae NCTC 8457]
 gi|183179415|ref|ZP_02957626.1| tRNA pseudouridine synthase A [Vibrio cholerae MZO-3]
 gi|227081173|ref|YP_002809724.1| tRNA pseudouridine synthase A [Vibrio cholerae M66-2]
 gi|229505402|ref|ZP_04394912.1| tRNA pseudouridine synthase A [Vibrio cholerae BX 330286]
 gi|229510928|ref|ZP_04400407.1| tRNA pseudouridine synthase A [Vibrio cholerae B33]
 gi|229518049|ref|ZP_04407493.1| tRNA pseudouridine synthase A [Vibrio cholerae RC9]
 gi|229529907|ref|ZP_04419297.1| tRNA pseudouridine synthase A [Vibrio cholerae 12129(1)]
 gi|229608421|ref|YP_002879069.1| tRNA pseudouridine synthase A [Vibrio cholerae MJ-1236]
 gi|254848129|ref|ZP_05237479.1| tRNA pseudouridine synthase A [Vibrio cholerae MO10]
 gi|255744781|ref|ZP_05418732.1| tRNA pseudouridine synthase A [Vibrio cholera CIRS 101]
 gi|262151270|ref|ZP_06028406.1| tRNA pseudouridine synthase A [Vibrio cholerae INDRE 91/1]
 gi|262167166|ref|ZP_06034879.1| tRNA pseudouridine synthase A [Vibrio cholerae RC27]
 gi|262190865|ref|ZP_06049084.1| tRNA pseudouridine synthase A [Vibrio cholerae CT 5369-93]
 gi|297578606|ref|ZP_06940534.1| tRNA pseudouridine synthase A [Vibrio cholerae RC385]
 gi|298498887|ref|ZP_07008694.1| tRNA pseudouridine synthase A [Vibrio cholerae MAK 757]
 gi|24212594|sp|Q9KTA4|TRUA_VIBCH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|172047415|sp|A5F2T4|TRUA_VIBC3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254764874|sp|C3LTP7|TRUA_VIBCM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|9655462|gb|AAF94160.1| tRNA pseudouridine synthase A [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121548411|gb|EAX58471.1| tRNA pseudouridine synthase A [Vibrio cholerae 2740-80]
 gi|126509619|gb|EAZ72213.1| tRNA pseudouridine synthase A [Vibrio cholerae NCTC 8457]
 gi|146316655|gb|ABQ21194.1| tRNA pseudouridine synthase A [Vibrio cholerae O395]
 gi|183012826|gb|EDT88126.1| tRNA pseudouridine synthase A [Vibrio cholerae MZO-3]
 gi|227009061|gb|ACP05273.1| tRNA pseudouridine synthase A [Vibrio cholerae M66-2]
 gi|227012816|gb|ACP09026.1| tRNA pseudouridine synthase A [Vibrio cholerae O395]
 gi|229333681|gb|EEN99167.1| tRNA pseudouridine synthase A [Vibrio cholerae 12129(1)]
 gi|229344764|gb|EEO09738.1| tRNA pseudouridine synthase A [Vibrio cholerae RC9]
 gi|229350893|gb|EEO15834.1| tRNA pseudouridine synthase A [Vibrio cholerae B33]
 gi|229357625|gb|EEO22542.1| tRNA pseudouridine synthase A [Vibrio cholerae BX 330286]
 gi|229371076|gb|ACQ61499.1| tRNA pseudouridine synthase A [Vibrio cholerae MJ-1236]
 gi|254843834|gb|EET22248.1| tRNA pseudouridine synthase A [Vibrio cholerae MO10]
 gi|255737812|gb|EET93206.1| tRNA pseudouridine synthase A [Vibrio cholera CIRS 101]
 gi|262024387|gb|EEY43075.1| tRNA pseudouridine synthase A [Vibrio cholerae RC27]
 gi|262030961|gb|EEY49589.1| tRNA pseudouridine synthase A [Vibrio cholerae INDRE 91/1]
 gi|262033256|gb|EEY51775.1| tRNA pseudouridine synthase A [Vibrio cholerae CT 5369-93]
 gi|297536200|gb|EFH75033.1| tRNA pseudouridine synthase A [Vibrio cholerae RC385]
 gi|297543220|gb|EFH79270.1| tRNA pseudouridine synthase A [Vibrio cholerae MAK 757]
          Length = 264

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 133/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGLY
Sbjct: 178 GRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 238 LVSVDY 243


>gi|251778715|ref|ZP_04821635.1| tRNA pseudouridine synthase A [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|243083030|gb|EES48920.1| tRNA pseudouridine synthase A [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 244

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 92/242 (38%), Positives = 133/242 (54%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIE++G+ + GWQRQ    ++QG +E AI  +TGE  + +G+ RTD GVHA   VA+F 
Sbjct: 6   LIIEFDGTNFCGWQRQVKDRTVQGCLENAILKITGEKSLTNGSSRTDGGVHAKAMVANF- 64

Query: 66  LVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +    +P     +ALN   K+ D ISI+    VD +FHAR+S+  + Y Y I+ R   LA
Sbjct: 65  ITNSSIPGEKFREALNT--KLPDDISIIKSEEVDMEFHARYSSKGKMYSYTIVNRYEKLA 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             K     + K L+ E+M+ A ++ VG+HDF  F S    A + +RTI  F +    N+I
Sbjct: 123 FGKQYLHHVRKELNVEDMKKACEYFVGKHDFKAFMSPGSSAKTTVRTITDFYIEENKNVI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FL+  +R  VG+L  VG GK    D+   +    RK  G   PP GL  + V
Sbjct: 183 RIFISADGFLYNMVRIIVGTLINVGTGKTKLQDVNNIINDGIRKNAGMCVPPNGLVLEKV 242

Query: 245 EY 246
            Y
Sbjct: 243 FY 244


>gi|229143213|ref|ZP_04271645.1| tRNA pseudouridine synthase A 2 [Bacillus cereus BDRD-ST24]
 gi|229177012|ref|ZP_04304407.1| tRNA pseudouridine synthase A 2 [Bacillus cereus 172560W]
 gi|228606487|gb|EEK63913.1| tRNA pseudouridine synthase A 2 [Bacillus cereus 172560W]
 gi|228640294|gb|EEK96692.1| tRNA pseudouridine synthase A 2 [Bacillus cereus BDRD-ST24]
          Length = 250

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|229015811|ref|ZP_04172787.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH1273]
 gi|229022018|ref|ZP_04178574.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH1272]
 gi|228739274|gb|EEL89714.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH1272]
 gi|228745470|gb|EEL95496.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH1273]
          Length = 250

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVQDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLEVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEGKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y +SVE+
Sbjct: 244 YLESVEF 250


>gi|146293537|ref|YP_001183961.1| tRNA pseudouridine synthase A [Shewanella putrefaciens CN-32]
 gi|166229836|sp|A4Y879|TRUA_SHEPC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|145565227|gb|ABP76162.1| tRNA pseudouridine synthase A [Shewanella putrefaciens CN-32]
 gi|319426837|gb|ADV54911.1| tRNA pseudouridine synthase A [Shewanella putrefaciens 200]
          Length = 261

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GSGYFGWQRQ    S+QG +E+A+ +V  E + +  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSGYFGWQRQAEVDSVQGQLERALSIVANEPIGLFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +NA   + D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFDTNAIRNEGAWTLGVNA--NLPDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +        ++D + M  AAQ L+G  DFT+FR++ CQ+ +P R +   +V   G
Sbjct: 119 RPGILRHGVSHYHGNIDADKMHQAAQVLLGEQDFTSFRAVQCQSKTPFRNVHCVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDIAANAFLHHMVRNIVGSLLEIGLGNQPLTWMGDLLALKDRNQAAATAKPHGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|82544799|ref|YP_408746.1| tRNA pseudouridine synthase A [Shigella boydii Sb227]
 gi|123728357|sp|Q31YE0|TRUA_SHIBS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|81246210|gb|ABB66918.1| pseudouridylate synthase I [Shigella boydii Sb227]
 gi|332093646|gb|EGI98704.1| tRNA pseudouridine synthase A [Shigella boydii 3594-74]
          Length = 270

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L   D I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  APRKDAAWTLGVNANL--PDDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|52144819|ref|YP_082010.1| tRNA pseudouridine synthase A [Bacillus cereus E33L]
 gi|62901422|sp|Q63GF1|TRUA2_BACCZ RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|51978288|gb|AAU19838.1| tRNA-pseudouridylate synthase I (tRNA pseudouridine synthase A)
           [Bacillus cereus E33L]
          Length = 245

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 141/247 (57%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYSLEVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPQILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|152984048|ref|YP_001347395.1| tRNA pseudouridine synthase A [Pseudomonas aeruginosa PA7]
 gi|150959206|gb|ABR81231.1| tRNA pseudouridine synthase A [Pseudomonas aeruginosa PA7]
          Length = 285

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 103/248 (41%), Positives = 137/248 (55%), Gaps = 9/248 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ+ G  S+Q ++E+A+  V  E V V  AGRTD+ VHA  QV
Sbjct: 19  RIALGVEYKGSRYRGWQRQEAGVPSVQEALERALSKVAAESVGVICAGRTDAAVHASGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT--- 118
            HFD   E          NA L     IS+    ++   FHARFSA+ R Y Y I     
Sbjct: 79  VHFDTAVERPLKAWVMGTNANL--PGDISVTWARVMPAHFHARFSAMARRYRYAIYNDPI 136

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R A +A E    W   + LD E MR AAQ LVG HDFT+FR++ CQA SP++T+ H  + 
Sbjct: 137 RPAHMAEEV--TW-NHRPLDIERMREAAQVLVGTHDFTSFRAVQCQARSPVKTMHHVRLL 193

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G LI + +   +FLH  +R+  G L  +G G+      ++ L+A+DR+  G  A P G
Sbjct: 194 EHGRLIVLDIRGNAFLHHMVRNIAGVLMTIGAGERPIEWAKEVLEARDRRAGGVTAHPYG 253

Query: 239 LYFDSVEY 246
           LY   VEY
Sbjct: 254 LYLVRVEY 261


>gi|75761576|ref|ZP_00741532.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|218895546|ref|YP_002443957.1| tRNA pseudouridine synthase A [Bacillus cereus G9842]
 gi|228899172|ref|ZP_04063442.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis IBL 4222]
 gi|228963570|ref|ZP_04124723.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|74490946|gb|EAO54206.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|218543347|gb|ACK95741.1| tRNA pseudouridine synthase A [Bacillus cereus G9842]
 gi|228796088|gb|EEM43543.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228860441|gb|EEN04831.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis IBL 4222]
          Length = 245

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|170754451|ref|YP_001781475.1| tRNA pseudouridine synthase A [Clostridium botulinum B1 str. Okra]
 gi|169119663|gb|ACA43499.1| tRNA pseudouridine synthase A [Clostridium botulinum B1 str. Okra]
          Length = 246

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 141/247 (57%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+TGE + +  +GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIASGRTDTGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTTFQCSTDEILNYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ +P++LD E M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHVPETLDIEAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + ++I  +   FLH  IR   G+L  +G     S D++  L+A+DR++ GP AP +GL
Sbjct: 179 KDSYVDIVYLGSGFLHKMIRILTGTLIEIGLHNLKSVDVKIILEAEDRRKAGPTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV+Y
Sbjct: 239 FMTSVDY 245


>gi|253988932|ref|YP_003040288.1| tRNA pseudouridine synthase A [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253780382|emb|CAQ83543.1| tRNA pseudouridine synthase A [Photorhabdus asymbiotica]
          Length = 264

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 139/246 (56%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+   SIQG +E+A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MKIALGIEYDGSQYYGWQRQQEVKSIQGCLEQALSKVADEPISVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF+   +         +NA+L     I++  +  VD+ FHARFSA  R Y Y I   R 
Sbjct: 61  VHFETSAQRKDAAWTMGVNAHLPAD--IAVRWVKTVDEDFHARFSATARRYRYIIFNHRY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G        LD + M  AAQ+L+G +DFT+FR++ CQ+ +P R + H +VN +
Sbjct: 119 RPAVLASGVTHFY-YPLDEKRMHQAAQYLLGENDFTSFRAVQCQSKTPWRNVMHINVNRY 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + I + A +F+H  +R+  GSL  +G G      + + L  +DR +    A   GLY
Sbjct: 178 GHYVVIDIKANAFVHHMVRNIAGSLMEIGCGNQDINWMARLLALKDRTKAAATAKSAGLY 237

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 238 LVAVDY 243


>gi|228950979|ref|ZP_04113100.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228808706|gb|EEM55204.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 250

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNLFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|150020829|ref|YP_001306183.1| tRNA pseudouridine synthase ACD [Thermosipho melanesiensis BI429]
 gi|166229846|sp|A6LLJ7|TRUA_THEM4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|149793350|gb|ABR30798.1| tRNA pseudouridine synthase A [Thermosipho melanesiensis BI429]
          Length = 244

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 143/246 (58%), Gaps = 6/246 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+ +   Y+G+ +FG+Q Q N  ++QG +EKA+  +  E +   GAGRTD+GVHA  Q
Sbjct: 1   MKRFAIEFSYDGTNFFGYQGQPNVRTVQGELEKALERIFKERIFTQGAGRTDAGVHANGQ 60

Query: 61  VAHFDLVREWVPVILCK-ALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           VA F+   + +  I  K ALNA L   + I +     V+K F+ RF A +R Y Y + T 
Sbjct: 61  VAAFNCPIDRLAAIDIKNALNANL--PEDIYVKKAWEVEKNFNPRFRAKKRIYHYLVSTN 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV-N 178
           +  +  ++   W     L+ E MRIAA++L G HDF++F+  + +  +PIRT+    + N
Sbjct: 119 EKDV-FKRNYVWHFKYKLNIEAMRIAARYLEGEHDFSSFKKGNDK-KNPIRTVYRIRILN 176

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
               LI IRV  RSFL + +R+ VGSL  VG G+WT   ++K L+A+ R+E    APP G
Sbjct: 177 VKKELILIRVEGRSFLRSMVRNIVGSLVRVGLGQWTPEKIKKVLEARSRQEAAGTAPPHG 236

Query: 239 LYFDSV 244
           LY   V
Sbjct: 237 LYLYKV 242


>gi|194099947|ref|YP_002003085.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae NCCP11945]
 gi|240017604|ref|ZP_04724144.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae FA6140]
 gi|240114197|ref|ZP_04728687.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae MS11]
 gi|240116830|ref|ZP_04730892.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID18]
 gi|254494689|ref|ZP_05107860.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae 1291]
 gi|268600271|ref|ZP_06134438.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae MS11]
 gi|268602508|ref|ZP_06136675.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID18]
 gi|238693230|sp|B4RR02|TRUA_NEIG2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|193935237|gb|ACF31061.1| TruA [Neisseria gonorrhoeae NCCP11945]
 gi|226513729|gb|EEH63074.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae 1291]
 gi|268584402|gb|EEZ49078.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae MS11]
 gi|268586639|gb|EEZ51315.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID18]
 gi|317165398|gb|ADV08939.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 265

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 134/245 (54%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+          + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDITAARPQQAWVRGVNAHLP--EGIAVLHARQVAPGFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA  L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAALLIGEQDFSSFRAAGCQAKSPVKTIYRTDLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|49476819|ref|YP_034755.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|62901429|sp|Q6HNW5|TRUA2_BACHK RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|49328375|gb|AAT59021.1| tRNA pseudouridine synthase I (tRNA pseudouridine synthase A)
           [Bacillus thuringiensis serovar konkukian str. 97-27]
          Length = 245

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+   + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKETEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHNRFHARYNSKVKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYSLEVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLAAEAIPQILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|332970287|gb|EGK09279.1| tRNA pseudouridine synthase A [Kingella kingae ATCC 23330]
          Length = 265

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 90/250 (36%), Positives = 138/250 (55%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS +FGWQ+Q +G  ++Q ++E A+  + GE +    AGRTD+GVHA  Q+
Sbjct: 8   RFALTVSYDGSQFFGWQKQADGVVTVQAALEHALSCIAGEPIATIAAGRTDTGVHATGQI 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      +  WV     + +NA+L   D +++L    V+  FHARF A  R Y Y +
Sbjct: 68  VHFDTQAHRPLSAWV-----RGVNAHLP--DGVAVLAAQAVEPAFHARFDATGRRYRYLL 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            +      L   RA     +L+ + M+ A   L+G HDF++FR+  CQA SPI+T+    
Sbjct: 121 ESAPVRSPLLYRRAGWTHYALNTDPMQAAMNLLLGEHDFSSFRAAQCQAKSPIKTMYAAQ 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +   G LI++   A +FLH  +R+ VG+L  VG G+ +  D    L  + R    P   P
Sbjct: 181 LQRAGCLIKLDFHANAFLHHMVRNLVGALVYVGCGRLSVADFADLLAQKSRLTAPPTFMP 240

Query: 237 EGLYFDSVEY 246
           +GLYF  V+Y
Sbjct: 241 DGLYFVGVDY 250


>gi|227114786|ref|ZP_03828442.1| tRNA pseudouridine synthase A [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 283

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 136/246 (55%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ + +S+Q  +EKA+  V  E + V  AGRTD+GVH   QV
Sbjct: 23  LKIALGIEYDGSLYYGWQRQIDVASVQACLEKALSKVADEPIEVFCAGRTDAGVHGTGQV 82

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF              +NA L     I++  +  VD+ FHARFSA  R Y Y I   R 
Sbjct: 83  VHFTTHAIRKDAAWTMGVNANLPPD--IAVRWVKTVDEDFHARFSATARRYRYVIYNHRY 140

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD E M  A Q L+G +DFT+FR++ CQ+ +P R ++H  V   
Sbjct: 141 RPAVLSRGMTHFY-HPLDVERMERAGQCLLGENDFTSFRAVQCQSRTPWRYVNHLKVTRH 199

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I + + A +F+H  +R+ VGSL  VG G    + + + L A+DR   G  A  EGLY
Sbjct: 200 GDYIVVDIKANAFVHHMVRNIVGSLMDVGCGNRPESWIAELLAAKDRTLAGATARAEGLY 259

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 260 LVAVDY 265


>gi|221134792|ref|ZP_03561095.1| tRNA pseudouridine synthase A [Glaciecola sp. HTCC2999]
          Length = 264

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 97/249 (38%), Positives = 134/249 (53%), Gaps = 16/249 (6%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
            M +EY G+ ++GWQRQ N  S+Q ++E A   V  E V +  +GRTD+GVHA  Q+ +F
Sbjct: 6   AMAVEYYGADFYGWQRQDNVPSVQQALEDAASFVADEKVNIICSGRTDAGVHATYQIVNF 65

Query: 65  DLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
                   + W        L    K  D I++     V   FHARFSA  R Y Y I   
Sbjct: 66  KTSAKRDEKAWT-------LGVTTKTPDAIAVKWAVEVPDTFHARFSATARRYRYIIYNH 118

Query: 120 QAPLA-LEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
           + P A L KG     +P  LD + M  AAQ LVG HDFT+FR+  CQ+ +P R I   +V
Sbjct: 119 RVPPAILAKGLTHCYLP--LDAQKMHEAAQVLVGEHDFTSFRAALCQSKTPFRNIHFVNV 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  + I + A +FLH  +R+  GSL L+G G+   + L++ L+ +DR + G  A P 
Sbjct: 177 QRVGEYVIIDIKANAFLHHMVRNIAGSLMLIGAGEQPLSWLQEILEIKDRTQAGVTAKPN 236

Query: 238 GLYFDSVEY 246
           GLYF  V+Y
Sbjct: 237 GLYFVDVDY 245


>gi|49183490|ref|YP_026742.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Sterne]
 gi|165870784|ref|ZP_02215437.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0488]
 gi|167634709|ref|ZP_02393028.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0442]
 gi|167640831|ref|ZP_02399090.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0193]
 gi|170688574|ref|ZP_02879780.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0465]
 gi|170707209|ref|ZP_02897665.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0389]
 gi|177654958|ref|ZP_02936652.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0174]
 gi|227816641|ref|YP_002816650.1| tRNA pseudouridine synthase A [Bacillus anthracis str. CDC 684]
 gi|229600408|ref|YP_002865093.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0248]
 gi|254686878|ref|ZP_05150736.1| tRNA pseudouridine synthase A [Bacillus anthracis str. CNEVA-9066]
 gi|254725958|ref|ZP_05187740.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A1055]
 gi|254738895|ref|ZP_05196597.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Western
           North America USA6153]
 gi|254743721|ref|ZP_05201406.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Kruger B]
 gi|254744486|ref|ZP_05202165.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Kruger B]
 gi|254756260|ref|ZP_05208289.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Vollum]
 gi|254762079|ref|ZP_05213928.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Australia
           94]
 gi|270000592|ref|YP_003329030.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Ames]
 gi|291612202|ref|YP_003541016.1| tRNA pseudouridine synthase A [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|62901431|sp|Q6I3T8|TRUA2_BACAN RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|49177417|gb|AAT52793.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Sterne]
 gi|164713618|gb|EDR19142.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0488]
 gi|167511225|gb|EDR86612.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0193]
 gi|167529783|gb|EDR92531.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0442]
 gi|170127987|gb|EDS96858.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0389]
 gi|170667434|gb|EDT18191.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0465]
 gi|172080343|gb|EDT65431.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0174]
 gi|224552835|gb|ACN55049.1| tRNA pseudouridine synthase A [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|227002712|gb|ACP12455.1| tRNA pseudouridine synthase A [Bacillus anthracis str. CDC 684]
 gi|229264816|gb|ACQ46453.1| tRNA pseudouridine synthase A [Bacillus anthracis str. A0248]
 gi|269850281|gb|ACZ49994.1| tRNA pseudouridine synthase A [Bacillus anthracis str. Ames]
          Length = 245

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+   + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKETEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYSLEVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLAAEAIPQILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|229188692|ref|ZP_04315731.1| tRNA pseudouridine synthase A 2 [Bacillus cereus ATCC 10876]
 gi|228594881|gb|EEK52661.1| tRNA pseudouridine synthase A 2 [Bacillus cereus ATCC 10876]
          Length = 250

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|329120625|ref|ZP_08249288.1| tRNA pseudouridine synthase A [Neisseria bacilliformis ATCC
           BAA-1200]
 gi|327460849|gb|EGF07183.1| tRNA pseudouridine synthase A [Neisseria bacilliformis ATCC
           BAA-1200]
          Length = 269

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 133/246 (54%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +I+ Y+GS +FGWQ+Q  G  ++Q ++E+A+  + GE + V  AGRTD+GVHA  QV
Sbjct: 8   RRALIVAYDGSRFFGWQKQAGGVPTVQAALEEALSGIAGERIAVTAAGRTDTGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E       +  N+ L   + +++L +  V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDTAAERPGQAWVRGTNSLLP--EGVAVLRVHNVPPHFHARFDACGRRYRYVLQSAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L  GRA      LD   MR AA  LVG HDF++FR+  CQA SP++T+    ++   
Sbjct: 126 RSPLLAGRAGWTHTPLDPAPMREAAALLVGTHDFSSFRAAECQAKSPVKTLYSVRLSGTA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + +   +FLH  +R+ VG+L  VG G+ +     + + A+ R +  P   P+GLY 
Sbjct: 186 RFMALDLHGNAFLHHMVRNIVGALVYVGSGRLSVAGFAELIAAKSRLKAPPTFMPDGLYL 245

Query: 242 DSVEYS 247
              +Y 
Sbjct: 246 TGADYP 251


>gi|260549154|ref|ZP_05823375.1| tRNA-pseudouridine synthase I [Acinetobacter sp. RUH2624]
 gi|260407882|gb|EEX01354.1| tRNA-pseudouridine synthase I [Acinetobacter sp. RUH2624]
          Length = 265

 Score =  163 bits (412), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 92/248 (37%), Positives = 134/248 (54%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKIADESIALHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD       +   +  N+  ++   ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTNAIRPEMGWLRGANS--QLPKDISIQWIKLMDENFHARFKATARRYRYVIYNA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H  +  
Sbjct: 119 PCRPALLHKQVTHIYQQLDVQKMIKAASKFEGTHNFETFRAAACQSNKPVRHVTHCRLFE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ VG L  +G G +    ++    AQDRK  G  APP+GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIVGCLLEIGQGMYEIDHIDTMFAAQDRKAAGVTAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQCYYP 246


>gi|77458123|ref|YP_347628.1| tRNA pseudouridine synthase A [Pseudomonas fluorescens Pf0-1]
 gi|77382126|gb|ABA73639.1| pseudouridylate synthase I [Pseudomonas fluorescens Pf0-1]
          Length = 274

 Score =  163 bits (412), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 96/252 (38%), Positives = 137/252 (54%), Gaps = 15/252 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
            R  + +EY GS Y GWQRQ  G  ++Q ++EKA+  V    + +  AGRTD+GVHA  Q
Sbjct: 7   FRVALGVEYKGSRYSGWQRQSTGVLTVQETLEKALSKVADSPISLQCAGRTDAGVHACGQ 66

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HFD      ++ WV       + A + +   IS+    I+   FHARF AI R Y Y 
Sbjct: 67  VVHFDTQVDRSLKAWV-------MGANINLPHDISVSWAKIMPAHFHARFKAIARRYRYV 119

Query: 116 IITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           I   Q  P  L +   W   + LD E M  AAQ+L+G HDF+ FR+  CQA SPI+ + H
Sbjct: 120 IYNDQIRPAHLNEEITW-NHRPLDVERMAEAAQYLIGTHDFSAFRAGQCQAKSPIKQMHH 178

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             V   G +I + + A +FLH  +R+  G L  +G G+     +++ L++++R+  G  A
Sbjct: 179 LRVTRHGKMIVLDIRANAFLHHMVRNIAGVLMTIGAGERPVEWMKEVLESRERRSGGVTA 238

Query: 235 PPEGLYFDSVEY 246
            P GLY   VEY
Sbjct: 239 HPFGLYLVQVEY 250


>gi|229042328|ref|ZP_04190078.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH676]
 gi|228726987|gb|EEL78194.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH676]
          Length = 250

 Score =  163 bits (412), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+   + G  RTD+GVHAL 
Sbjct: 6   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKETEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|109897925|ref|YP_661180.1| tRNA pseudouridine synthase A [Pseudoalteromonas atlantica T6c]
 gi|123064742|sp|Q15VG2|TRUA_PSEA6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|109700206|gb|ABG40126.1| tRNA pseudouridine synthase A [Pseudoalteromonas atlantica T6c]
          Length = 263

 Score =  163 bits (412), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 93/245 (37%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G+ + GWQRQ    S+Q  +E+A+  +  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGVEYDGARFHGWQRQNEVISVQQHLEEALTRIANEPIRVVCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +N YL   DTIS+  +  V + FHARFSA  R Y Y I     
Sbjct: 61  VHFETTSQRPDRAWTLGINTYL--PDTISVRWVKAVPEDFHARFSATARRYRYIIYNNTL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +       I   LD E M  AAQ LVG+HDF++FR+++CQA +  RT+ H  V   G
Sbjct: 119 RSGILANGVTHIYGDLDHELMHEAAQKLVGKHDFSSFRAVNCQAKTATRTMSHIRVKRMG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I I V A +FLH  +R+  G+L  +G  +     +++ L+ +DR + G  A P GLY 
Sbjct: 179 DYIVIDVQANAFLHHMVRNITGTLVAIGHKEKPVEWVDELLEVKDRTKAGITALPNGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VHVTY 243


>gi|229077782|ref|ZP_04210409.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock4-2]
 gi|228705510|gb|EEL57869.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock4-2]
          Length = 245

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HL+G HDFT F +   +  S +R +   DV  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKAAAKHLIGSHDFTAFSNAKSKKKSMVREVYTLDVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|229165426|ref|ZP_04293210.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH621]
 gi|228618024|gb|EEK75065.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH621]
          Length = 268

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 24  MNNYKLTIQYDGARYKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 83

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI ++  V  +FHAR+++  ++YLY+I   
Sbjct: 84  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITSVEEVPDRFHARYNSKAKTYLYKIWNE 141

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV+ 
Sbjct: 142 EHTNPFMRKYSMHVNKQLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVSE 201

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 202 ESGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLEADAIPNILEEKQRNQINCLAEASGL 261

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 262 YLENVEF 268


>gi|114046997|ref|YP_737547.1| tRNA pseudouridine synthase A [Shewanella sp. MR-7]
 gi|123131546|sp|Q0HWL5|TRUA_SHESR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|113888439|gb|ABI42490.1| tRNA pseudouridine synthase A [Shewanella sp. MR-7]
          Length = 261

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 93/245 (37%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GSGYFGWQRQ    S+QG +E+A+  V  E + +  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSGYFGWQRQAEVDSVQGQLEQALSKVANEPISLFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA L   D I++     VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETNAIRNEGAWTLGVNANLP--DNIAVRWAKEVDDSFHARFSATARRYRYVIYNHNF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         +D + M +AAQ L+G  DFT+FR+I CQ+ +P R +    V   G
Sbjct: 119 RPGILRHGVSHYHGDIDADKMHVAAQALLGEQDFTSFRAIQCQSKTPFRNVHSVKVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDISANAFLHHMVRNIVGSLLEIGLGNQPLTWMADLLALKDRNQAAATAKPNGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|153216039|ref|ZP_01950244.1| tRNA pseudouridine synthase A [Vibrio cholerae 1587]
 gi|153829544|ref|ZP_01982211.1| tRNA pseudouridine synthase A [Vibrio cholerae 623-39]
 gi|254226230|ref|ZP_04919824.1| tRNA pseudouridine synthase A [Vibrio cholerae V51]
 gi|254291873|ref|ZP_04962656.1| tRNA pseudouridine synthase A [Vibrio cholerae AM-19226]
 gi|124114489|gb|EAY33309.1| tRNA pseudouridine synthase A [Vibrio cholerae 1587]
 gi|125621266|gb|EAZ49606.1| tRNA pseudouridine synthase A [Vibrio cholerae V51]
 gi|148875004|gb|EDL73139.1| tRNA pseudouridine synthase A [Vibrio cholerae 623-39]
 gi|150422233|gb|EDN14197.1| tRNA pseudouridine synthase A [Vibrio cholerae AM-19226]
 gi|327483717|gb|AEA78124.1| tRNA pseudouridine synthase A [Vibrio cholerae LMA3894-4]
          Length = 264

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 133/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTSAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGLY
Sbjct: 178 GRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 238 LVSVDY 243


>gi|153939803|ref|YP_001391236.1| tRNA pseudouridine synthase A [Clostridium botulinum F str.
           Langeland]
 gi|152935699|gb|ABS41197.1| tRNA pseudouridine synthase A [Clostridium botulinum F str.
           Langeland]
          Length = 246

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+TGE + +  +GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIASGRTDTGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTTFQGSTDEILSYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ +P++LD E M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHVPETLDIEAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + +  +   FLH  IR   G+L  VG     S D++  L+A+DR++ GP AP +GL
Sbjct: 179 KDGYVNLVYLGSGFLHKMIRILTGTLIEVGLHNLKSVDVKNILKAEDRRKAGPTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV+Y
Sbjct: 239 FMTSVDY 245


>gi|229154192|ref|ZP_04282315.1| tRNA pseudouridine synthase A 2 [Bacillus cereus ATCC 4342]
 gi|228629282|gb|EEK85986.1| tRNA pseudouridine synthase A 2 [Bacillus cereus ATCC 4342]
          Length = 250

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  +  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MYNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVVSEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLEVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+A+ R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPHILEAKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|295700767|ref|YP_003608660.1| tRNA pseudouridine synthase A [Burkholderia sp. CCGE1002]
 gi|295439980|gb|ADG19149.1| tRNA pseudouridine synthase A [Burkholderia sp. CCGE1002]
          Length = 270

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + ++Y+G+ + GWQ Q +G+++Q  +E+A+   T   V    AGRTD GVH L Q
Sbjct: 1   MKRIALGVQYDGAAFAGWQSQPHGNTVQDELERALREFTRTPVQTVVAGRTDRGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   + V +   +  NA+L    TI +     +   FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELDRVDISWVRGPNAFLP--KTIGVQWAKPMPDDFHARFSAFERTYYYVLYVSP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   RA  +   LD + MR AA+HL+G HDF+ FRS  CQ+ +P + +   DV   
Sbjct: 119 VRSPMLTTRAGWVHTPLDVDAMRSAAEHLIGEHDFSAFRSSQCQSKTPFKHLYRIDVKRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN +  R  A +FLH  +R+ +G L  +G G+  +  +   L ++ R    P   P+GLY
Sbjct: 179 GNFVHFRFRANAFLHHMVRNVMGCLIEIGSGRRPAAWMADVLASRSRDCAAPTFMPDGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAQVGY 244


>gi|254362514|ref|ZP_04978619.1| tRNA-pseudouridine synthase I [Mannheimia haemolytica PHL213]
 gi|153094111|gb|EDN75015.1| tRNA-pseudouridine synthase I [Mannheimia haemolytica PHL213]
          Length = 261

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 93/252 (36%), Positives = 140/252 (55%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ+   S+Q  +E+A+ +V    V V  AGRTD+GVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQEAVESVQQQLEQALSVVANSPVEVFCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+          C   NA+L   D I++     V++ FHARFSA  R Y Y I     
Sbjct: 61  VHFETQANRPLQSWCFGTNAHL--PDDIAVKWAVAVNEDFHARFSATARRYRYIIFN--- 115

Query: 122 PLALEKGRAWLIPKS-------LDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
               +K R+ ++PK        LD   M  A Q+L+G +DF++FR+  CQ+++P R I H
Sbjct: 116 ----QKLRSAILPKGVTHFHFPLDERKMHQAGQYLLGENDFSSFRAAKCQSNTPWRNIHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V+  GN + + + A +F+H  +R+ VG+L  +G G+      +  L+ +DR++  P A
Sbjct: 172 LNVSRQGNYVIVDIQANAFVHHMVRNIVGTLLEIGQGRQPVEWAKWVLEQRDREKAAPTA 231

Query: 235 PPEGLYFDSVEY 246
             EGLY   V Y
Sbjct: 232 KAEGLYLVEVHY 243


>gi|225862468|ref|YP_002747846.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB102]
 gi|225790549|gb|ACO30766.1| tRNA pseudouridine synthase A [Bacillus cereus 03BB102]
          Length = 245

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYSLEVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+A+ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPHILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|15677859|ref|NP_275027.1| tRNA pseudouridine synthase A [Neisseria meningitidis MC58]
 gi|25009507|sp|Q9JXI2|TRUA_NEIMB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|7227297|gb|AAF42357.1| tRNA pseudouridine synthase A [Neisseria meningitidis MC58]
 gi|316983916|gb|EFV62895.1| tRNA pseudouridine synthase A [Neisseria meningitidis H44/76]
 gi|325201083|gb|ADY96538.1| tRNA pseudouridine synthase A [Neisseria meningitidis H44/76]
          Length = 265

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 134/245 (54%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIGQMRQAAALLVGEQDFSSFRAAECQAKSPVKTIYRADLTQSS 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|262280848|ref|ZP_06058631.1| tRNA-pseudouridine synthase I [Acinetobacter calcoaceticus RUH2202]
 gi|262257748|gb|EEY76483.1| tRNA-pseudouridine synthase I [Acinetobacter calcoaceticus RUH2202]
          Length = 265

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 92/248 (37%), Positives = 133/248 (53%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE+ +  V  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKVANEPIALHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD           +  N+  ++   ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTHAIRPETGWLRGANS--QLPKDISIQWIKLMDESFHARFKATARRYRYIIYNT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   I + LD + M  AA    G H+F +FR+  CQ++ P+R + H  +  
Sbjct: 119 PHRPALLHKQVTHIYQPLDVQKMIEAASKFEGTHNFESFRAAACQSNQPVRHVKHCRLFE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ VG L  +G G +    ++    AQDRK  G  APP+GL
Sbjct: 179 HGRYLVLDIQADGFLHHMVRNIVGCLLEIGQGMYEINHIDAMFAAQDRKAAGVTAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQCNYP 246


>gi|331091743|ref|ZP_08340575.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330402642|gb|EGG82209.1| tRNA pseudouridine synthase A [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 245

 Score =  162 bits (410), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 133/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I Y+G+ Y GWQ Q NG +I+  + KA+  +TGE +VV GA RTDSGVHA+  
Sbjct: 1   MRRVKLTIAYDGTNYCGWQIQPNGITIEEIVNKALSKLTGEKIVVIGASRTDSGVHAMGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD      P  +  A+N  L   + I ++    V   FH R+    ++Y Y I+  +
Sbjct: 61  VAVFDTETTIPPERVAMAVNRIL--PEDIVVVKSEEVPLDFHPRYCDCEKTYEYHIVNTR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  ++   + +   LD + MR  A +L+G HDF +F +I     S +RT+   ++   
Sbjct: 119 IPIPTKRLTNYFVSYELDLDKMREGASYLIGEHDFASFCNIKTDVESTVRTVKELEILEN 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I IR+    FL+  +R  VG+L  VG G +    +++ L+A++RK  G  APP GL 
Sbjct: 179 GEEITIRISGNGFLYNMVRIIVGTLIRVGRGFYEPVQVKEILEAKNRKAAGVTAPPHGLM 238

Query: 241 FDSVEYS 247
              + Y+
Sbjct: 239 LMEIRYN 245


>gi|257092844|ref|YP_003166485.1| tRNA pseudouridine synthase A [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
 gi|257045368|gb|ACV34556.1| tRNA pseudouridine synthase A [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
          Length = 266

 Score =  162 bits (410), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+GSG+ GWQ Q  G ++Q +++ A+    G  V V  AGRTD+GVHA  QV
Sbjct: 1   MRIALAVEYDGSGFRGWQTQPGGGTVQDAVQDALRQFAGVPVQVVSAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   E       +  N++L     +++     V   FHARFSA  R Y Y +I R  
Sbjct: 61  VHFDAAVERSMFAWVRGTNSFLP--SAVAVRWARPVADDFHARFSAYARRYRYLLINRAH 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +  GR       LD   M+ AA  L+G  DF+ FR+  CQA+SP++ +    V  FG
Sbjct: 119 RTGVWNGRVGWYHHPLDVGTMQAAAHLLLGERDFSAFRAAECQANSPVKVMREAHVRRFG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           +LI     A +FLH  +R+ VGSL  VG GK     + + L A DR+   P     GLY 
Sbjct: 179 DLIAFDFEASAFLHHMVRNLVGSLVHVGQGKRPPEWIGELLAAGDRRLAAPTFAAAGLYL 238

Query: 242 DSVEY 246
            +V Y
Sbjct: 239 FAVRY 243


>gi|168184901|ref|ZP_02619565.1| tRNA pseudouridine synthase A [Clostridium botulinum Bf]
 gi|237795344|ref|YP_002862896.1| tRNA pseudouridine synthase A [Clostridium botulinum Ba4 str. 657]
 gi|182672019|gb|EDT83980.1| tRNA pseudouridine synthase A [Clostridium botulinum Bf]
 gi|229263868|gb|ACQ54901.1| tRNA pseudouridine synthase A [Clostridium botulinum Ba4 str. 657]
          Length = 246

 Score =  162 bits (410), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+TGE + +  +GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIASGRTDTGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTTFQGSTDEILNYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ IP++LD   M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHIPETLDINAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +++  +   FLH  IR   G+L  VG     S D++  L+A+DR++ GP AP +GL
Sbjct: 179 KDGYVDLVYLGSGFLHKMIRILTGTLIEVGLHNLKSVDVKNILEAEDRRKAGPTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV+Y
Sbjct: 239 FMTSVDY 245


>gi|269102116|ref|ZP_06154813.1| tRNA pseudouridine synthase A [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268162014|gb|EEZ40510.1| tRNA pseudouridine synthase A [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 261

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 95/245 (38%), Positives = 136/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ YFGWQRQ+   S+Q  +EKA+  +  E V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGAKYFGWQRQREVDSVQERLEKALAKIANEPVDVFCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+            +NA+L  SD I++   + V   FHARF+A  R Y Y I     
Sbjct: 61  VHFDVNVNRKMAAWTMGVNAHLP-SD-IAVRWAAEVSDDFHARFTATARRYRYVIYNHAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q+L+G +DFT+FR++HCQ+ SP R + H +V+  G
Sbjct: 119 RPAILSSGVSHYHGDLDEKKMHEAGQYLLGENDFTSFRAVHCQSRSPWRNLMHLNVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N + I + A +F+H  +R+  GSL  VG G+     ++  L+ +DR   G  A  EGLY 
Sbjct: 179 NYVIIDIKANAFVHHMVRNITGSLIKVGRGEEKPEWIKWLLEQKDRTLAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|117919927|ref|YP_869119.1| tRNA pseudouridine synthase A [Shewanella sp. ANA-3]
 gi|166229837|sp|A0KV94|TRUA_SHESA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|117612259|gb|ABK47713.1| tRNA pseudouridine synthase A [Shewanella sp. ANA-3]
          Length = 261

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 93/245 (37%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GSGYFGWQRQ    S+QG +E+A+  V  E + +  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSGYFGWQRQAEVDSVQGQLEQALSKVANEPISLFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA L   D I++     VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETNAIRNEGAWTLGVNANL--PDNIAVRWAKEVDDTFHARFSATARRYRYVIYNHNF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         +D + M +AAQ L+G  DFT+FR+I CQ+ +P R +    V   G
Sbjct: 119 RPGILRHGVSHYHGDIDTDKMHVAAQALLGEQDFTSFRAIQCQSKTPFRNVHSVKVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDISANAFLHHMVRNIVGSLLEIGLGNQPLTWMADLLALKDRNQAAATAKPNGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|87121856|ref|ZP_01077742.1| tRNA-pseudouridine synthase I [Marinomonas sp. MED121]
 gi|86162885|gb|EAQ64164.1| tRNA-pseudouridine synthase I [Marinomonas sp. MED121]
          Length = 275

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 138/246 (56%), Gaps = 5/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +  +++EY GS Y GWQ QK +  ++Q  +E+A+  +    + V  AGRTD+ VHA  QV
Sbjct: 5   KVALVVEYKGSEYKGWQAQKYDVPTVQKCLEEALSKIAAHTIKVVCAGRTDASVHASAQV 64

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   E         +N+ L     I+++  + +   FHARFSA+ R Y Y I +   
Sbjct: 65  VHFETDVERSERAWTLGVNSNL--PKDIAVVAAANMHPSFHARFSAVSRRYRYVIYSHPL 122

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  + K   W   K LD   M+ AA+  VG+HDF++FR++ CQA +P+RTI +F++   
Sbjct: 123 RPAIMSKEVTW-THKKLDILKMQQAAKVFVGKHDFSSFRAVGCQAHTPVRTILNFEIYQS 181

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  I + + A +FLH  IR+F G L  +G G+   +   K L A+DR + G   PPEGLY
Sbjct: 182 GQYIVLDIRANAFLHHMIRNFAGVLMTIGAGEEEVSWASKVLAAKDRTKGGITGPPEGLY 241

Query: 241 FDSVEY 246
           F   EY
Sbjct: 242 FVDAEY 247


>gi|187921475|ref|YP_001890507.1| tRNA pseudouridine synthase A [Burkholderia phytofirmans PsJN]
 gi|238691591|sp|B2T9N4|TRUA_BURPP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|187719913|gb|ACD21136.1| tRNA pseudouridine synthase A [Burkholderia phytofirmans PsJN]
          Length = 270

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 132/246 (53%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + ++Y+GS + GWQ Q + +++Q  +E+A+       V    AGRTD+GVH L Q
Sbjct: 1   MKRIALGVQYDGSAFCGWQSQPHRNTVQDELERALREFARTPVQTVVAGRTDTGVHGLGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD   +   V   +  N++L    TIS+     +  +FHARFSA  R+Y Y +    
Sbjct: 61  VVHFDTELDRADVSWVRGTNSFLP--KTISVQWAKPMPDEFHARFSAFERTYYYVLYVHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
               +   RA  +  SLD + M+ AA HL+G HDF+ FRS  CQA +P++ +   DV   
Sbjct: 119 VRSPMLATRAGWVHTSLDVDAMQKAAAHLLGEHDFSAFRSSQCQAKTPVKHLYQIDVKQQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ +  R  A +FLH  +R+ +G L  +G G+     + + L ++DR    P   P+GLY
Sbjct: 179 GDFVHFRFRANAFLHHMVRNLMGCLVYIGGGRRPVEWMAEVLASRDRDFAAPTFMPDGLY 238

Query: 241 FDSVEY 246
              V Y
Sbjct: 239 LAQVGY 244


>gi|229009911|ref|ZP_04167130.1| tRNA pseudouridine synthase A 2 [Bacillus mycoides DSM 2048]
 gi|229131424|ref|ZP_04260320.1| tRNA pseudouridine synthase A 2 [Bacillus cereus BDRD-ST196]
 gi|228652008|gb|EEL07949.1| tRNA pseudouridine synthase A 2 [Bacillus cereus BDRD-ST196]
 gi|228751342|gb|EEM01149.1| tRNA pseudouridine synthase A 2 [Bacillus mycoides DSM 2048]
          Length = 268

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 24  MNNYKLTIQYDGARYKGWQRLGNNDNTIQGKIESIISEMVGKEIEIIGCSRTDAGVHALN 83

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI ++  V  +FHAR+++  ++YLY+I   
Sbjct: 84  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITSVEEVPDRFHARYNSKAKTYLYKIWNE 141

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV+ 
Sbjct: 142 EHTNPFMRKYSMHVNKQLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVSE 201

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 202 ESGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLEADAIPNILEEKQRNQINCLAEASGL 261

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 262 YLENVEF 268


>gi|330810793|ref|YP_004355255.1| tRNA-pseudouridine synthase I [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327378901|gb|AEA70251.1| tRNA-pseudouridine synthase I [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 284

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 137/251 (54%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EYNGS Y GWQRQ +G  ++Q ++E A+  V    V +H AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYNGSRYRGWQRQASGVLTVQETLENALSKVADSPVSLHCAGRTDAGVHACGQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTQVERSMKAWV-------MGANINLPHDVSVSWAKVMPAHFHARFKAIARRYRYVI 130

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AAQ+LVG HDF+ FR+  CQA SPI+ + H 
Sbjct: 131 YNDQIRPAHLNEEITW-NHRPLDVERMAEAAQYLVGVHDFSAFRAGQCQAKSPIKELHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I + + A +FLH  +R+  G L  +G G+     +++ L ++ R+  G  A 
Sbjct: 190 RVTRHGKMIVLDIRASAFLHHMVRNIAGVLMTIGAGERPVEWIKEVLDSRIRRSGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PFGLYLVQVEY 260


>gi|148379875|ref|YP_001254416.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. ATCC
           3502]
 gi|153930931|ref|YP_001384172.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. ATCC
           19397]
 gi|153935153|ref|YP_001387713.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. Hall]
 gi|148289359|emb|CAL83455.1| tRNA pseudouridine synthase [Clostridium botulinum A str. ATCC
           3502]
 gi|152926975|gb|ABS32475.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. ATCC
           19397]
 gi|152931067|gb|ABS36566.1| tRNA pseudouridine synthase A [Clostridium botulinum A str. Hall]
          Length = 246

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+TGE + +  +GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIASGRTDTGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTTFQGSTDEILSYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ +P++LD E M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHVPETLDIEAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
             + ++I  +   FLH  IR   G+L  +G     S D++  L A+DR++ GP AP +GL
Sbjct: 179 KDSYVDIVYLGSGFLHKMIRILTGTLIEIGLHNLKSVDVKIILDAEDRRKAGPTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV+Y
Sbjct: 239 FMTSVDY 245


>gi|42779623|ref|NP_976870.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10987]
 gi|51316696|sp|Q73E17|TRUA2_BACC1 RecName: Full=tRNA pseudouridine synthase A 2; AltName: Full=tRNA
           pseudouridylate synthase I 2; AltName: Full=tRNA-uridine
           isomerase I 2
 gi|42735539|gb|AAS39478.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 10987]
          Length = 245

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+   + G  RTD+GVHAL 
Sbjct: 1   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKETEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLEVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPQILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|292488882|ref|YP_003531769.1| pseudouridylate synthase I [Erwinia amylovora CFBP1430]
 gi|292900028|ref|YP_003539397.1| tRNA pseudouridine synthase A [Erwinia amylovora ATCC 49946]
 gi|291199876|emb|CBJ47000.1| tRNA pseudouridine synthase A [Erwinia amylovora ATCC 49946]
 gi|291554316|emb|CBA21677.1| pseudouridylate synthase I [Erwinia amylovora CFBP1430]
 gi|312173042|emb|CBX81297.1| pseudouridylate synthase I [Erwinia amylovora ATCC BAA-2158]
          Length = 271

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 135/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V    + V  AGRTD+GVH+  QV
Sbjct: 11  MKLALGIEYDGSRYYGWQRQNEVRSVQEKLEKALTRVADGPIAVFCAGRTDAGVHSTGQV 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +NA L     I++  +  V   FHARFSA  R Y Y I  R+ 
Sbjct: 71  VHFETTAQRKDAAWTLGVNANLPAD--IAVRWVKSVPDDFHARFSATARRYRYVIYNRRL 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD E M+ A Q L+G +DFT+FR++ CQ+ +P+R + H +V+  G
Sbjct: 129 RPAILAAGVTHFYHPLDVEKMQSAGQCLLGENDFTSFRAVQCQSRTPMRNVMHLNVSRHG 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  +G G    + + + L A+DRK     A  EGLY 
Sbjct: 189 AYVVVDIKANAFVHHMVRNIVGSLMEIGCGNQPESWMSELLAAKDRKLAAATARAEGLYL 248

Query: 242 DSVEY 246
            +V+Y
Sbjct: 249 VAVDY 253


>gi|113969768|ref|YP_733561.1| tRNA pseudouridine synthase A [Shewanella sp. MR-4]
 gi|123325149|sp|Q0HKB3|TRUA_SHESM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|113884452|gb|ABI38504.1| tRNA pseudouridine synthase A [Shewanella sp. MR-4]
          Length = 261

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GSGYFGWQRQ    S+QG +E+A+  V  E + +  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSGYFGWQRQAEVDSVQGQLEQALSKVANEPISLFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA L   D I++     VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETNAIRNEGAWTLGVNANLP--DNIAVRWAKEVDDSFHARFSATARRYRYVIYNHNF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         +D + M +AAQ L+G  DFT+FR++ CQ+ +P R +    V   G
Sbjct: 119 RPGILRHGVSHYHGDIDADKMHVAAQALLGEQDFTSFRAVQCQSKTPFRNVHSVKVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDISANAFLHHMVRNIVGSLLEIGLGNQPLTWMADLLALKDRNQAAATAKPNGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|188590732|ref|YP_001919706.1| tRNA pseudouridine synthase A [Clostridium botulinum E3 str. Alaska
           E43]
 gi|238689635|sp|B2UYE4|TRUA_CLOBA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|188501013|gb|ACD54149.1| tRNA pseudouridine synthase A [Clostridium botulinum E3 str. Alaska
           E43]
          Length = 244

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 91/242 (37%), Positives = 133/242 (54%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIE++G+ + GWQRQ    ++QG +E AI  +TGE  + +G+ RTD GVHA   VA+F 
Sbjct: 6   LIIEFDGTNFCGWQRQVKDRTVQGCLENAILKITGEKSLTNGSSRTDGGVHAKAMVANF- 64

Query: 66  LVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +    +P     +ALN   K+ D ISI+    VD +FHAR+S+  + Y Y I+ R   LA
Sbjct: 65  ITNSSIPGEKFREALNT--KLPDDISIIKSEEVDMEFHARYSSKGKMYSYTIVNRYEKLA 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             K     + K L+ E+M+ A ++ +G+HDF  F S    A + +RTI  F +    N+I
Sbjct: 123 FGKQYLHHVRKELNVEDMKKACEYFLGKHDFKAFMSPGSSAKTTVRTITDFYIEENKNVI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
            I + A  FL+  +R  VG+L  VG GK    D+   +    RK  G   PP GL  + V
Sbjct: 183 RIFISADGFLYNMVRIIVGTLINVGTGKTKLQDVNNIINDGIRKNAGMCVPPNGLVLEKV 242

Query: 245 EY 246
            Y
Sbjct: 243 FY 244


>gi|228956904|ref|ZP_04118685.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228802747|gb|EEM49583.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 250

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G  + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MHNYKLTIQYDGVRFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPNILEEKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|229148825|ref|ZP_04277073.1| tRNA pseudouridine synthase A 2 [Bacillus cereus m1550]
 gi|228634619|gb|EEK91200.1| tRNA pseudouridine synthase A 2 [Bacillus cereus m1550]
          Length = 250

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MHNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKAAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+     +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDVEAIPNILEEKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|15598310|ref|NP_251804.1| tRNA pseudouridine synthase A [Pseudomonas aeruginosa PAO1]
 gi|107102663|ref|ZP_01366581.1| hypothetical protein PaerPA_01003728 [Pseudomonas aeruginosa PACS2]
 gi|218890685|ref|YP_002439549.1| tRNA pseudouridine synthase A [Pseudomonas aeruginosa LESB58]
 gi|254236084|ref|ZP_04929407.1| tRNA-pseudouridine synthase I [Pseudomonas aeruginosa C3719]
 gi|254241809|ref|ZP_04935131.1| tRNA-pseudouridine synthase I [Pseudomonas aeruginosa 2192]
 gi|296388384|ref|ZP_06877859.1| tRNA pseudouridine synthase A [Pseudomonas aeruginosa PAb1]
 gi|313108437|ref|ZP_07794441.1| tRNA-pseudouridine synthase I [Pseudomonas aeruginosa 39016]
 gi|8134770|sp|O87016|TRUA_PSEAE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|9949225|gb|AAG06502.1|AE004735_9 tRNA-pseudouridine synthase I [Pseudomonas aeruginosa PAO1]
 gi|3237313|gb|AAC23941.1| HisT [Pseudomonas aeruginosa PAO1]
 gi|126168015|gb|EAZ53526.1| tRNA-pseudouridine synthase I [Pseudomonas aeruginosa C3719]
 gi|126195187|gb|EAZ59250.1| tRNA-pseudouridine synthase I [Pseudomonas aeruginosa 2192]
 gi|218770908|emb|CAW26673.1| tRNA-pseudouridine synthase I [Pseudomonas aeruginosa LESB58]
 gi|310880943|gb|EFQ39537.1| tRNA-pseudouridine synthase I [Pseudomonas aeruginosa 39016]
          Length = 285

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 104/249 (41%), Positives = 136/249 (54%), Gaps = 9/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + IEY GS Y GWQRQ+ G  S+Q ++E+A+  V  E V V  AGRTD+ VHA  QV
Sbjct: 19  RIALGIEYKGSRYRGWQRQEAGVPSVQEALERALSKVAAEPVGVICAGRTDAAVHASGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT--- 118
            HFD   E          NA L     IS+    ++   FHARFSA+ R Y Y I     
Sbjct: 79  VHFDTAVERPLKAWVMGTNANLPAD--ISVTWARVMPAHFHARFSAMARRYRYAIYNDPI 136

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R A LA E    W   + LD   MR AAQ LVG HDFT+FR++ CQA SP++T+ H  + 
Sbjct: 137 RPAHLAEEV--TWNH-RPLDIGRMREAAQVLVGTHDFTSFRAVQCQAKSPVKTMHHVRLL 193

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G LI + +   +FLH  +R+  G L  +G G+      ++ L+A+DR+  G  A P G
Sbjct: 194 EHGRLIVLDIRGNAFLHHMVRNIAGVLMTIGAGERPIEWAKEVLEARDRRAGGVTAHPYG 253

Query: 239 LYFDSVEYS 247
           LY   VEY 
Sbjct: 254 LYLVRVEYP 262


>gi|319789624|ref|YP_004151257.1| tRNA pseudouridine synthase A [Thermovibrio ammonificans HB-1]
 gi|317114126|gb|ADU96616.1| tRNA pseudouridine synthase A [Thermovibrio ammonificans HB-1]
          Length = 254

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 138/251 (54%), Gaps = 7/251 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  + + +EY G+ Y+GWQ   +  ++QG I + +  V    V + GA RTD+GVHA  Q
Sbjct: 1   MRNFKLTVEYLGTNYYGWQFLPDKPTVQGEIIRCLETVLRHPVKLIGASRTDAGVHARGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA+F   +E     L  ALN  L     I +  +  V  +FHAR SA  + Y YR+  R 
Sbjct: 61  VANFLTAKEVSCEKLLSALNGLL--PPDIRVKEVEEVPLEFHARRSARGKLYRYRLFIRD 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTF-RSIHCQASSPIRTIDHFDVNS 179
            P   E  R+W + ++L  E MR A Q LVG HDFTTF +S   +  +PIRTID  ++ +
Sbjct: 119 VPSPFEFRRSWYLRRTLSVEPMREATQFLVGTHDFTTFSKSERKREVNPIRTIDKIEITN 178

Query: 180 F----GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
                G L+E+    RSFL   +R  V +L  VG G+    ++++ LQA+DR     LAP
Sbjct: 179 KEWEEGVLVELLFTGRSFLRHMVRVIVATLVKVGTGEVKPQEVKEMLQAKDRSRAPFLAP 238

Query: 236 PEGLYFDSVEY 246
           P+GLY + V Y
Sbjct: 239 PDGLYLERVFY 249


>gi|163938417|ref|YP_001643301.1| tRNA pseudouridine synthase A [Bacillus weihenstephanensis KBAB4]
 gi|163860614|gb|ABY41673.1| tRNA pseudouridine synthase A [Bacillus weihenstephanensis KBAB4]
          Length = 245

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARYKGWQRLGNNDNTIQGKIESIISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI ++  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITSVEEVPDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV+ 
Sbjct: 119 EHTNPFMRKYSMHVNKQLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVSE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 179 ESGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLEADAIPNILEEKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|323977481|gb|EGB72567.1| tRNA pseudouridine synthase A [Escherichia coli TW10509]
          Length = 270

 Score =  162 bits (409), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGANNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|161869166|ref|YP_001598332.1| tRNA pseudouridine synthase A [Neisseria meningitidis 053442]
 gi|189030137|sp|A9M0B8|TRUA_NEIM0 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|161594719|gb|ABX72379.1| tRNA pseudouridine synthase [Neisseria meningitidis 053442]
          Length = 265

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 90/250 (36%), Positives = 138/250 (55%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQV 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      V+ WV     + +NA+L   + I++L+   V  +FHARF A  R Y Y +
Sbjct: 68  VHFDTAAVRPVQAWV-----RGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLL 120

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
            +      L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D
Sbjct: 121 ESAPVRSPLLKNRAGWTHLKLDIGQMRQAAALLIGEQDFSSFRAAECQAKSPVKTIYRAD 180

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           +     L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P
Sbjct: 181 LTQSSGLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMP 240

Query: 237 EGLYFDSVEY 246
           +GLY   V+Y
Sbjct: 241 DGLYLTGVDY 250


>gi|330829261|ref|YP_004392213.1| tRNA pseudouridine synthase A [Aeromonas veronii B565]
 gi|328804397|gb|AEB49596.1| tRNA pseudouridine synthase A [Aeromonas veronii B565]
          Length = 269

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 94/245 (38%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ+   S+Q  +E A+  +    V +  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSRYFGWQRQREVISVQAELETALSRIANHPVSIQCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             LN+ L     I++  +  VD+ FHARFSA  R Y Y I     
Sbjct: 61  IHFDTEANRAEGAWTLGLNSNLP--PDIAVRWVKQVDESFHARFSATARRYRYVIYNHNY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+         ++++ E M  A Q L+G HDF+TFR++ CQ+++P R + H  V+  G
Sbjct: 119 RPAILGSGVSHYHETINAELMHQAGQSLLGEHDFSTFRAVACQSNTPWRNVTHLCVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+  GSL LVG G      + + L A+DR   GP A   GLY 
Sbjct: 179 PYIVLDIRANAFLHHMVRNITGSLLLVGQGLKPVEWIAEVLAAKDRNLAGPTAKAGGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|261346179|ref|ZP_05973823.1| tRNA pseudouridine synthase A [Providencia rustigianii DSM 4541]
 gi|282565835|gb|EFB71370.1| tRNA pseudouridine synthase A [Providencia rustigianii DSM 4541]
          Length = 271

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 137/247 (55%), Gaps = 4/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + R  + IEYNGS Y+GWQRQ+   S+QG +E+A+  +  E + V+ AGRTD+GVHA  Q
Sbjct: 7   LYRIALGIEYNGSRYYGWQRQQEVKSVQGCLEEALSKIAAEPISVNCAGRTDAGVHATGQ 66

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-R 119
           V HF+              N +L     I++     VD++FHARFSA  R Y Y I   R
Sbjct: 67  VVHFETTAIRKEAAWTMGANTHL--PPDIAVRWCKPVDEEFHARFSATARRYRYVIFNHR 124

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
             P  L  G        LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V  
Sbjct: 125 YRPAILSNGVTHF-HYPLDEKRMHQAAQALLGENDFTSFRAVQCQSRTPWRNVMHVNVTR 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            GN + + + A +F+H  +R+ VGSL  +G G      + + L+ +DR +    A  EGL
Sbjct: 184 HGNYVVVDIKANAFVHHMVRNIVGSLLEIGCGNQDIDWMHQLLELKDRTKAAATAKAEGL 243

Query: 240 YFDSVEY 246
           Y  SV+Y
Sbjct: 244 YLVSVDY 250


>gi|229083731|ref|ZP_04216052.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock3-44]
 gi|228699589|gb|EEL52253.1| tRNA pseudouridine synthase A 2 [Bacillus cereus Rock3-44]
          Length = 268

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y   I+Y+G+ Y GWQR   N ++IQG IE  +  + G+ + + G  RTD+GVHAL 
Sbjct: 24  MNNYKFTIQYDGARYKGWQRLGNNDNTIQGKIESVLSEMVGQEIEIIGCSRTDAGVHALN 83

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F +  +     + K LN YL   + ISI ++  V ++FHAR+++  ++YLY+I   
Sbjct: 84  QVANFKIEEKLSEPKVKKYLNQYL--PNDISITDVEQVPERFHARYNSKAKTYLYKIWNE 141

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ E+M+ AAQ+L+G HDFT F +   +  S +R +   DV  
Sbjct: 142 EHTNPFMRKYSMHVQKKLNIESMQKAAQYLIGSHDFTAFSNAKSKKKSMVREVYMLDVAE 201

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               I+IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 202 SEGFIQIRVSGNGFLHNMVRKIVGALVEVGLGQLDADAIPQILEAKQRNQINCLADASGL 261

Query: 240 YFDSVEY 246
           Y + V++
Sbjct: 262 YLEKVDF 268


>gi|92113385|ref|YP_573313.1| tRNA pseudouridine synthase A [Chromohalobacter salexigens DSM
           3043]
 gi|91796475|gb|ABE58614.1| tRNA pseudouridine synthase A [Chromohalobacter salexigens DSM
           3043]
          Length = 290

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 94/244 (38%), Positives = 134/244 (54%), Gaps = 8/244 (3%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           M +EY+GS Y GWQR K+ +S+QG++E A+  +    V V  +GRTDSGVHA RQV HFD
Sbjct: 1   MGVEYDGSAYCGWQRLKHAASVQGTLEAALSRIANAPVQVLCSGRTDSGVHATRQVVHFD 60

Query: 66  LVREWVPVILCKA---LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
                 PV   +      A   +   +++  +  V   FHAR SA+ R Y Y I+ + + 
Sbjct: 61  -----APVTRTQKAWLFGANANLPRDVAVRWVVPVADDFHARLSALARRYRYVILNQPSR 115

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
             LE+  A    + LD E M  AAQ LVG HDF++FR+  CQ+ S  R +   +V  +G 
Sbjct: 116 PVLERANATWCREPLDAERMHAAAQALVGEHDFSSFRAAGCQSKSRWRHVHFIEVRRYGQ 175

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           L+ I + A +FLH  IR+  G+L  VG G  ++  L + L  +DR +    AP  GL+F 
Sbjct: 176 LVVIDIQANAFLHHMIRNIAGALVAVGRGDHSTGYLGELLALRDRTQGNVTAPGCGLHFV 235

Query: 243 SVEY 246
              Y
Sbjct: 236 DALY 239


>gi|119775285|ref|YP_928025.1| tRNA pseudouridine synthase A [Shewanella amazonensis SB2B]
 gi|166229832|sp|A1S7J9|TRUA_SHEAM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|119767785|gb|ABM00356.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
          Length = 261

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 136/251 (54%), Gaps = 14/251 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS ++GWQRQ   +S+Q  +E+A+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSKFYGWQRQAEVNSVQAELERALSIVANEPIEVQCAGRTDAGVHATGQV 60

Query: 62  AHFDL--VRE---WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD   VR+   W        L   + + D I++     V+  FHARFSA  R Y Y I
Sbjct: 61  VHFDTNAVRKEGAWT-------LGVNVHLPDDIAVRWAMPVNDDFHARFSATARRYRYVI 113

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
                 P  L KG +      +D E M  AAQ L+G  DFT+FR+I CQ+++P R +   
Sbjct: 114 FNHNFRPGILRKGVSHY-HGDIDVERMHDAAQALIGERDFTSFRAIGCQSNTPFRNVHKV 172

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V+  G  I + + A +FLH  +R+ VGSL  +G G      +   L+A+DR +    A 
Sbjct: 173 SVSRHGMYIVVDIQANAFLHHMVRNIVGSLLEIGLGNQPLDWMATLLEAKDRSQAAATAK 232

Query: 236 PEGLYFDSVEY 246
           P GLY   V Y
Sbjct: 233 PHGLYLVDVTY 243


>gi|301156483|emb|CBW15954.1| pseudouridylate synthase I [Haemophilus parainfluenzae T3T1]
          Length = 264

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 95/257 (36%), Positives = 136/257 (52%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y GWQRQ+   S+Q  +EKA+  V  E + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYNGKQYCGWQRQEKVRSVQEELEKALSFVANEKIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+       + W       A      + D IS+    +VD +FHARFSA  R Y Y  
Sbjct: 61  VHFETTAVRPEKAW-------AFGTNANLPDDISVSWAKVVDDEFHARFSATARRYRY-- 111

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                 L   K R+ ++P+        LD + M  A Q L+G +DF++FR+  CQ+++P 
Sbjct: 112 -----ILYCNKLRSAILPEGITHCHLDLDEKKMHQAGQFLLGENDFSSFRAAQCQSNTPW 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R + H +V   G  + + + A +F+H  +R+ VGSL  VG G      ++  L+ +DRK 
Sbjct: 167 RNVHHLNVVRKGQFVIVDIQANAFVHHMVRNIVGSLIEVGAGNQPVEWMKWLLEQKDRKL 226

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A PEGLY  +V Y
Sbjct: 227 AAPTAKPEGLYLVNVIY 243


>gi|299771694|ref|YP_003733720.1| tRNA pseudouridine synthase A [Acinetobacter sp. DR1]
 gi|298701782|gb|ADI92347.1| tRNA pseudouridine synthase A [Acinetobacter sp. DR1]
          Length = 265

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 92/248 (37%), Positives = 133/248 (53%), Gaps = 3/248 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE+ +  V  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGVQYRGWQTQQPGVASVQETIERVLSKVANEPIALHGAGRTDAGVHATN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            VAHFD           +  N+  ++   ISI  + ++D+ FHARF A  R Y Y I   
Sbjct: 61  MVAHFDTHAIRPETGWLRGANS--QLPKDISIQWIKLMDESFHARFKATARRYRYIIYNT 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL   +   I + LD + M  AA    G H+F +FR+  CQ++ P+R + H  +  
Sbjct: 119 PHRPALLHKQVTHIYQKLDVKKMIEAASKFEGTHNFESFRAAACQSNQPVRHVKHCRLFE 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + + + A  FLH  +R+ VG L  +G G +    ++    AQDRK  G  APP+GL
Sbjct: 179 HGRYLVLDIEADGFLHHMVRNIVGCLLEIGQGMYEIDHIDTMFAAQDRKAAGVTAPPDGL 238

Query: 240 YFDSVEYS 247
           YF    Y 
Sbjct: 239 YFIQCNYP 246


>gi|40063298|gb|AAR38116.1| tRNA pseudouridine synthase A [uncultured marine bacterium 578]
          Length = 247

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 93/252 (36%), Positives = 140/252 (55%), Gaps = 15/252 (5%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           ++  + +EY G+ + GWQ QK+G  ++Q  +E A+ LV    V V   GRTDSGVHA  Q
Sbjct: 1   MKIALGVEYLGTNFNGWQIQKSGIRTVQEVVESALSLVANHPVRVFCCGRTDSGVHAKEQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HF+         WV           + +   ++      VD  FHARF+A  RSY Y+
Sbjct: 61  VIHFETDSNRSNEAWV-------FGGNVNLPSDVNFSWAKDVDDDFHARFNAYARSYEYK 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I       +L        P+SL+ + MR AA  L+G HDF++FR   CQA SP++T+++ 
Sbjct: 114 IHNHPVRSSLNANYYLWEPRSLNIDEMRKAANFLIGEHDFSSFRGRLCQAKSPVKTVEYL 173

Query: 176 DV-NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
           D+  S  NLI +++ A +FLH  +R+ VG+L  +G G+  +  +   L+++DR+E GP A
Sbjct: 174 DIIESDDNLI-VKIKANAFLHHMVRNIVGTLLKIGRGERDAEWMLSVLESKDRREAGPTA 232

Query: 235 PPEGLYFDSVEY 246
            P+GLYF    Y
Sbjct: 233 EPQGLYFIKAYY 244


>gi|325135431|gb|EGC58051.1| tRNA pseudouridine synthase A [Neisseria meningitidis M0579]
          Length = 265

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 134/245 (54%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGESVATTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKHRAGWTHLKLDIGQMRQAAALLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|295319272|gb|ADF99649.1| tRNA pseudouridine synthase A [Clostridium botulinum F str. 230613]
          Length = 246

 Score =  162 bits (409), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+TGE + +  +GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIASGRTDTGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTTFQGSTDEILSYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ +P++LD E M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHVPETLDIEAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               + +  +   FLH  IR   G+L  VG     S D +  L+A+DR++ GP AP +GL
Sbjct: 179 KDGYVNLVYLGSGFLHKMIRILTGTLIEVGLHNLKSVDCKNILKAEDRRKAGPTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV+Y
Sbjct: 239 FMTSVDY 245


>gi|258622013|ref|ZP_05717042.1| tRNA pseudouridine synthase A [Vibrio mimicus VM573]
 gi|258585766|gb|EEW10486.1| tRNA pseudouridine synthase A [Vibrio mimicus VM573]
          Length = 264

 Score =  162 bits (409), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 133/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     +++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDVAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R I H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNIMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY
Sbjct: 178 GRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVEVDY 243


>gi|153001275|ref|YP_001366956.1| tRNA pseudouridine synthase A [Shewanella baltica OS185]
 gi|166229834|sp|A6WQ04|TRUA_SHEB8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|151365893|gb|ABS08893.1| tRNA pseudouridine synthase A [Shewanella baltica OS185]
          Length = 261

 Score =  161 bits (408), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 130/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+GYFGWQRQ    S+QG +E+A+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGNGYFGWQRQAEVDSVQGQLERALSIVANEPIGVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA   + D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETNAIRNEGAWTLGVNA--NLPDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         +D + M  AAQ L+G  DFT+FR++ CQ+ +P R +   +V   G
Sbjct: 119 RPGILRHGVSHYHGDIDADRMHQAAQALLGEQDFTSFRAVQCQSKTPFRNVHCVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDIAANAFLHHMVRNIVGSLLEIGLGNQPLTWMGDLLALKDRNQAAATAKPHGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|50121981|ref|YP_051148.1| tRNA pseudouridine synthase A [Pectobacterium atrosepticum
           SCRI1043]
 gi|62901300|sp|Q6D2N7|TRUA_ERWCT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|49612507|emb|CAG75957.1| tRNA pseudouridine synthase A [Pectobacterium atrosepticum
           SCRI1043]
          Length = 283

 Score =  161 bits (408), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ + +S+Q  +EKA+  V  E + V  AGRTD+GVH   QV
Sbjct: 23  LKIALGIEYDGSQYYGWQRQIDVASVQACLEKALSKVADEPIEVLCAGRTDAGVHGTGQV 82

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF              +NA L     I++  +  V + FHARFSA  R Y Y I   R 
Sbjct: 83  VHFTTQAIRKDAAWTMGVNANL--PPDIAVRWVKAVHEDFHARFSATARRYRYIIYNHRY 140

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G        LD E M  A Q L+G +DFT+FR++ CQ+ +P R ++H  V   
Sbjct: 141 RPAVLSHGMTHFY-HPLDVERMERAGQCLLGENDFTSFRAVQCQSRTPWRNVNHLKVTRH 199

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN I + + A +F+H  +R+ VGSL  VG G    + + + L A+DR   G  A  EGLY
Sbjct: 200 GNYIVVDIKANAFVHHMVRNIVGSLMDVGCGNRPESWIAELLAAKDRTLAGATARAEGLY 259

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 260 LVAVDY 265


>gi|118594739|ref|ZP_01552086.1| tRNA pseudouridine synthase A [Methylophilales bacterium HTCC2181]
 gi|118440517|gb|EAV47144.1| tRNA pseudouridine synthase A [Methylophilales bacterium HTCC2181]
          Length = 264

 Score =  161 bits (408), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 128/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R    + YNG G+ GWQ+Q +  +IQG IE A+  +  + V+ H +GRTDSGVHAL Q+
Sbjct: 1   MRIACSVSYNGYGFSGWQKQPDVKTIQGLIESALTEIAKDTVITHASGRTDSGVHALGQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD  +        K +NA+L  S  I +     + + FHAR S + R Y Y +I    
Sbjct: 61  IHFDTTKNRPLTAWVKGVNAFLPSS--IKVRWAKNISESFHARHSVLEREYQYLLIKDTN 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+    A      LD  N+  A +   G HDF++FRS  CQA SP+RTI+ F    FG
Sbjct: 119 NSAIFHATAGWTYFDLDDYNLMAACKCFEGTHDFSSFRSSECQAKSPVRTINQFRCEQFG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           N     + A  FLH QIR+ + ++  V   + +   ++  L  +DR    P   P GLY 
Sbjct: 179 NTYLFTIRANGFLHHQIRNMIAAVIHVAKNEDSVGFIDDLLSKKDRTLAPPTFMPNGLYL 238

Query: 242 DSVEY 246
            +++Y
Sbjct: 239 SNIKY 243


>gi|258627102|ref|ZP_05721898.1| tRNA pseudouridine synthase A [Vibrio mimicus VM603]
 gi|258580620|gb|EEW05573.1| tRNA pseudouridine synthase A [Vibrio mimicus VM603]
          Length = 264

 Score =  161 bits (408), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 133/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     +++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDVAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R I H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNIMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY
Sbjct: 178 GRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVEVDY 243


>gi|324324528|gb|ADY19788.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 245

 Score =  161 bits (408), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITNVEEVQDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLEVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+++ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPHILESKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|237653725|ref|YP_002890039.1| tRNA pseudouridine synthase A [Thauera sp. MZ1T]
 gi|237624972|gb|ACR01662.1| tRNA pseudouridine synthase A [Thauera sp. MZ1T]
          Length = 265

 Score =  161 bits (408), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 128/247 (51%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + +EY G  + GWQ Q +G ++Q  +E+A+  + GE V  H AGRTD+GVHA  Q
Sbjct: 1   MRRIVLGLEYAGDAFCGWQSQAHGRTVQDVLERALAQIAGEPVRTHCAGRTDTGVHASAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VAHFD           + +NA L     + +   + V   FHARF A  R Y Y +    
Sbjct: 61  VAHFDTRAVRPASAWVRGVNALLP--PAVVVRWSTEVGDDFHARFLACERQYRYILHNAP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+  GR      +LD E M  AAQ LVG HDF++FR+  CQA +P+R +    V   
Sbjct: 119 TRPAMLAGRVGWYHPALDVERMAAAAQCLVGTHDFSSFRAAGCQAKTPVRVMHEARVVRQ 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  +     A  FLH  IR+ VG+L  VG G++    + + L+A+DR    P   P+GLY
Sbjct: 179 GEYLLFDFRANGFLHHMIRNLVGALVYVGKGRYPVAWMRELLEARDRARAAPTFSPDGLY 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LCGVAYP 245


>gi|169797325|ref|YP_001715118.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AYE]
 gi|213155861|ref|YP_002317906.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AB0057]
 gi|215484762|ref|YP_002326997.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AB307-0294]
 gi|301346428|ref|ZP_07227169.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AB056]
 gi|301511754|ref|ZP_07236991.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AB058]
 gi|301594287|ref|ZP_07239295.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AB059]
 gi|332852976|ref|ZP_08434486.1| tRNA pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332866410|ref|ZP_08436994.1| tRNA pseudouridine synthase A [Acinetobacter baumannii 6013113]
 gi|226708639|sp|B7H0S9|TRUA_ACIB3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226708640|sp|B7I4E8|TRUA_ACIB5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238688022|sp|B0V4L0|TRUA_ACIBY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|169150252|emb|CAM88148.1| tRNA-pseudouridine synthase I [Acinetobacter baumannii AYE]
 gi|213055021|gb|ACJ39923.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AB0057]
 gi|213988479|gb|ACJ58778.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AB307-0294]
 gi|332728912|gb|EGJ60267.1| tRNA pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332734636|gb|EGJ65742.1| tRNA pseudouridine synthase A [Acinetobacter baumannii 6013113]
          Length = 265

 Score =  161 bits (408), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 135/253 (53%), Gaps = 13/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIERVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       + A  ++   ISI  +  +D++FHARF A  R Y Y
Sbjct: 61  MVAHFDTTAIRPERGWI-------MGANSQLPKDISIQWIKQMDEEFHARFKATARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H
Sbjct: 114 VVYNAPHRPALLHKQVTHIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DRK  G  A
Sbjct: 174 CRLFQHGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDTMFAAEDRKAAGITA 233

Query: 235 PPEGLYFDSVEYS 247
           PP+GLYF    Y 
Sbjct: 234 PPDGLYFIQCYYP 246


>gi|218548227|ref|YP_002382018.1| tRNA pseudouridine synthase A [Escherichia fergusonii ATCC 35469]
 gi|226708655|sp|B7LLF2|TRUA_ESCF3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|218355768|emb|CAQ88381.1| pseudouridylate synthase I [Escherichia fergusonii ATCC 35469]
 gi|324112855|gb|EGC06831.1| tRNA pseudouridine synthase A [Escherichia fergusonii B253]
 gi|325496642|gb|EGC94501.1| tRNA pseudouridine synthase A [Escherichia fergusonii ECD227]
          Length = 270

 Score =  161 bits (408), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSRYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGANNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|196040200|ref|ZP_03107502.1| tRNA pseudouridine synthase A [Bacillus cereus NVH0597-99]
 gi|196029055|gb|EDX67660.1| tRNA pseudouridine synthase A [Bacillus cereus NVH0597-99]
          Length = 245

 Score =  161 bits (408), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 141/247 (57%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 1   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN +L   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 61  QVANFQSDEKLVEHKVKKYLNQHL--PNDISITNVEEVHDRFHARYNSKAKTYLYKIWNE 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 119 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYSLEVME 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  + + L+A+ R +   LA   GL
Sbjct: 179 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLAAEAIPQILEAKQRNQINCLAEASGL 238

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 239 YLENVEF 245


>gi|150015077|ref|YP_001307331.1| tRNA pseudouridine synthase A [Clostridium beijerinckii NCIMB 8052]
 gi|189030131|sp|A6LPU5|TRUA_CLOB8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|149901542|gb|ABR32375.1| tRNA pseudouridine synthase A [Clostridium beijerinckii NCIMB 8052]
          Length = 244

 Score =  161 bits (408), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 89/242 (36%), Positives = 137/242 (56%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIE++GS + GWQRQ  G +IQ  IE AIF  TGE ++++G+ RTD+GVHA   VA+F 
Sbjct: 6   LIIEFDGSNFCGWQRQPKGRTIQKVIETAIFKATGEEIMINGSSRTDAGVHAREMVANF- 64

Query: 66  LVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           L    +P     +A+N   ++ + +SI+    V + FHAR+S+  ++Y Y II R   L+
Sbjct: 65  LTNSSIPGDKFREAINT--RLPEDVSIIKSEEVSEDFHARYSSKGKTYSYTIINRYERLS 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
           L     +     LD   MR A ++ +GRHDF  F S      +  RTI    ++  GN I
Sbjct: 123 LGHQYLYHYKYRLDVNEMRRACEYFIGRHDFRAFMSPGSSIKTTTRTIHDLYIDQNGNEI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I + A  FL+  +R  VG+L  +G+GK    +++  ++  +RK+ G   PP GL  + V
Sbjct: 183 KIFITADGFLYNMVRIIVGTLIKIGNGKLEVENIKDIIEEGNRKKAGMCVPPNGLILEKV 242

Query: 245 EY 246
            Y
Sbjct: 243 FY 244


>gi|237732351|ref|ZP_04562832.1| tRNA pseudouridine synthase A [Citrobacter sp. 30_2]
 gi|226907890|gb|EEH93808.1| tRNA pseudouridine synthase A [Citrobacter sp. 30_2]
          Length = 270

 Score =  161 bits (408), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANERINVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLG 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V  FG  + +
Sbjct: 134 KGVTHYY-EPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHIKVERFGAYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGANNQPESWIAELLAARDRTLAAATAKAEGLYLVAVDY 252


>gi|262171995|ref|ZP_06039673.1| tRNA pseudouridine synthase A [Vibrio mimicus MB-451]
 gi|261893071|gb|EEY39057.1| tRNA pseudouridine synthase A [Vibrio mimicus MB-451]
          Length = 264

 Score =  161 bits (408), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 133/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     +++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDVAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY
Sbjct: 178 GRYVVIDIKANAFVHHMVRNITGSLITVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVEVDY 243


>gi|91200879|emb|CAJ73934.1| strongly similar to tRNA pseudouridine synthase I [Candidatus
           Kuenenia stuttgartiensis]
          Length = 244

 Score =  161 bits (408), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 89/241 (36%), Positives = 134/241 (55%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY G+ Y GWQ QKN  S+Q ++  A+  V  E V +HGAGRTD+GVHAL QVA+F 
Sbjct: 6   LTIEYEGTNYAGWQWQKNAISVQETLTHAVRTVIREEVEIHGAGRTDAGVHALGQVANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                    L +A+N +L     I+I +++ +++ FHAR+SA  + Y Y ++      +L
Sbjct: 66  TYSAIPAKQLLRAINFHL--PQDITIKDVADMEEGFHARYSATSKVYRYTVLNDWLRTSL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   ++    LD   M  AAQ+L+G HDFT+F +        IRTI + ++   G  I 
Sbjct: 124 NRNFCYVYGFPLDLSKMMTAAQYLIGTHDFTSFTTKALDNKDRIRTIKNLEIQKEGKYIY 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             V A  FL+  +R+ VG+L  +G GK     + K L+  +R + GP AP +GL    V+
Sbjct: 184 FVVEANGFLYKMVRTIVGTLLEIGRGKMDVYLIRKLLETGNRDDAGPTAPAKGLCMKEVK 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|325578129|ref|ZP_08148264.1| tRNA pseudouridine synthase A [Haemophilus parainfluenzae ATCC
           33392]
 gi|325159865|gb|EGC71994.1| tRNA pseudouridine synthase A [Haemophilus parainfluenzae ATCC
           33392]
          Length = 264

 Score =  161 bits (408), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 95/257 (36%), Positives = 136/257 (52%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y GWQRQ+   S+Q  +EKA+  V  E + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYNGKQYCGWQRQEKVRSVQEELEKALSFVANEKIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+       + W       A      + D IS+    +VD +FHARFSA  R Y Y  
Sbjct: 61  VHFETTAVRPEKAW-------AFGTNANLPDDISVSWAKVVDDEFHARFSATARRYRY-- 111

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                 L   K R+ ++P+        LD + M  A Q L+G +DF++FR+  CQ+++P 
Sbjct: 112 -----ILYCNKLRSAILPEGITHCHLDLDEKKMHQAGQFLLGENDFSSFRAAQCQSNTPW 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R + H +V   G  + + + A +F+H  +R+ VGSL  VG G      ++  L+ +DRK 
Sbjct: 167 RNVHHLNVVRKGQYVIVDIQANAFVHHMVRNIVGSLIEVGAGNQPVEWMKWLLEQKDRKL 226

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A PEGLY  +V Y
Sbjct: 227 AAPTAKPEGLYLVNVIY 243


>gi|229028278|ref|ZP_04184414.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH1271]
 gi|228733042|gb|EEL83888.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH1271]
          Length = 250

 Score =  161 bits (408), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 140/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + IS+ ++  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISVTDVEEVPDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+A+ R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDAEAIPYILEAKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|307131844|ref|YP_003883860.1| tRNA pseudouridine synthase A [Dickeya dadantii 3937]
 gi|306529373|gb|ADM99303.1| tRNA pseudouridine synthase A [Dickeya dadantii 3937]
          Length = 276

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 95/247 (38%), Positives = 136/247 (55%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ    S+QG +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 13  LKIALGIEYDGSRYYGWQRQAEVDSVQGCLEAALSQVANERIDVFCAGRTDAGVHATGQV 72

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            HF              +NA L     I++  +  VD  FHARFSA  R Y Y I  R+ 
Sbjct: 73  VHFTTRAARKDAAWTMGVNANLPPD--IAVRWVKTVDDAFHARFSATARRYRYVIYNRRF 130

Query: 121 APLALEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P  L +G   + +P  LD E M  A Q L+G +DFT+FR++ CQ+ +P R + H  V  
Sbjct: 131 RPAILSRGVTHYYLP--LDAERMHRAGQCLLGENDFTSFRAVQCQSRTPWRNLMHLRVAR 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + + + A +F+H  +R+ VGSL  +G G  +   + + L A+DR      A  +GL
Sbjct: 189 QGDYVVVDIKANAFVHHMVRNIVGSLMEIGCGNQSENWMAELLAAKDRTLAAATAKADGL 248

Query: 240 YFDSVEY 246
           Y  SV+Y
Sbjct: 249 YLVSVDY 255


>gi|183599662|ref|ZP_02961155.1| hypothetical protein PROSTU_03151 [Providencia stuartii ATCC 25827]
 gi|188021916|gb|EDU59956.1| hypothetical protein PROSTU_03151 [Providencia stuartii ATCC 25827]
          Length = 271

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 97/248 (39%), Positives = 137/248 (55%), Gaps = 10/248 (4%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEYNGS Y+GWQRQ+   S+QG +E A+  V    + V  AGRTD+GVHA  QV 
Sbjct: 9   RIALGIEYNGSRYYGWQRQQEVKSVQGCLEDALSKVANHPINVFCAGRTDAGVHATGQVV 68

Query: 63  HFDLVREWVPVILCKA---LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT- 118
           HFD      PVI  +A   +     + + I++     VD++FHARFSA  R Y Y I   
Sbjct: 69  HFD-----TPVIRKEAAWTMGVNTHLPEDIAVRWCKPVDEEFHARFSATARRYRYVIFNH 123

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R  P  L  G        LD + M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V 
Sbjct: 124 RYRPAILSSGVTHF-HYPLDEKKMHEAAQALLGENDFTSFRAVQCQSRTPWRNVMHVQVT 182

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             GN + + + A +F+H  +R+ VGSL  +G G      + + L+ +DR +    A  +G
Sbjct: 183 RHGNYVVVDIKANAFVHHMVRNIVGSLLEIGCGNQDINWMAQLLELKDRTKAAATAKADG 242

Query: 239 LYFDSVEY 246
           LY  SV+Y
Sbjct: 243 LYLVSVDY 250


>gi|15802865|ref|NP_288892.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 EDL933]
 gi|15832456|ref|NP_311229.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. Sakai]
 gi|26248707|ref|NP_754747.1| tRNA pseudouridine synthase A [Escherichia coli CFT073]
 gi|82777729|ref|YP_404078.1| tRNA pseudouridine synthase A [Shigella dysenteriae Sd197]
 gi|168748172|ref|ZP_02773194.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4113]
 gi|168755075|ref|ZP_02780082.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4401]
 gi|168761239|ref|ZP_02786246.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4501]
 gi|168767949|ref|ZP_02792956.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4486]
 gi|168772951|ref|ZP_02797958.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4196]
 gi|168780178|ref|ZP_02805185.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4076]
 gi|168787230|ref|ZP_02812237.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC869]
 gi|168798493|ref|ZP_02823500.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC508]
 gi|170680088|ref|YP_001744518.1| tRNA pseudouridine synthase A [Escherichia coli SMS-3-5]
 gi|195935697|ref|ZP_03081079.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4024]
 gi|208807895|ref|ZP_03250232.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4206]
 gi|208811862|ref|ZP_03253191.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821544|ref|ZP_03261864.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4042]
 gi|209397276|ref|YP_002271727.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4115]
 gi|217327172|ref|ZP_03443255.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           TW14588]
 gi|218695917|ref|YP_002403584.1| tRNA pseudouridine synthase A [Escherichia coli 55989]
 gi|218700794|ref|YP_002408423.1| tRNA pseudouridine synthase A [Escherichia coli IAI39]
 gi|218705848|ref|YP_002413367.1| tRNA pseudouridine synthase A [Escherichia coli UMN026]
 gi|227887378|ref|ZP_04005183.1| tRNA pseudouridine synthase A [Escherichia coli 83972]
 gi|254794211|ref|YP_003079048.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           TW14359]
 gi|261223227|ref|ZP_05937508.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261259223|ref|ZP_05951756.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291283559|ref|YP_003500377.1| tRNA pseudouridine synthase A [Escherichia coli O55:H7 str. CB9615]
 gi|293405784|ref|ZP_06649776.1| tRNA pseudouridine synthase A [Escherichia coli FVEC1412]
 gi|293410675|ref|ZP_06654251.1| tRNA pseudouridine synthase A [Escherichia coli B354]
 gi|293415611|ref|ZP_06658254.1| tRNA pseudouridine synthase A [Escherichia coli B185]
 gi|293446655|ref|ZP_06663077.1| tRNA pseudouridine synthase A [Escherichia coli B088]
 gi|298381467|ref|ZP_06991066.1| tRNA pseudouridine synthase A [Escherichia coli FVEC1302]
 gi|300822193|ref|ZP_07102335.1| tRNA pseudouridine synthase A [Escherichia coli MS 119-7]
 gi|300936897|ref|ZP_07151784.1| tRNA pseudouridine synthase A [Escherichia coli MS 21-1]
 gi|300983542|ref|ZP_07176636.1| tRNA pseudouridine synthase A [Escherichia coli MS 45-1]
 gi|301024150|ref|ZP_07187860.1| tRNA pseudouridine synthase A [Escherichia coli MS 69-1]
 gi|301049077|ref|ZP_07196061.1| tRNA pseudouridine synthase A [Escherichia coli MS 185-1]
 gi|301303220|ref|ZP_07209345.1| tRNA pseudouridine synthase A [Escherichia coli MS 124-1]
 gi|307311121|ref|ZP_07590765.1| tRNA pseudouridine synthase A [Escherichia coli W]
 gi|309784972|ref|ZP_07679605.1| tRNA pseudouridine synthase A [Shigella dysenteriae 1617]
 gi|309793201|ref|ZP_07687629.1| tRNA pseudouridine synthase A [Escherichia coli MS 145-7]
 gi|331663835|ref|ZP_08364745.1| tRNA pseudouridine synthase A [Escherichia coli TA143]
 gi|331669017|ref|ZP_08369865.1| tRNA pseudouridine synthase A [Escherichia coli TA271]
 gi|331673820|ref|ZP_08374583.1| tRNA pseudouridine synthase A [Escherichia coli TA280]
 gi|331678264|ref|ZP_08378939.1| tRNA pseudouridine synthase A [Escherichia coli H591]
 gi|54039780|sp|P65845|TRUA_ECO57 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|54042085|sp|P65844|TRUA_ECOL6 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123755724|sp|Q32DL8|TRUA_SHIDS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226708651|sp|B7NNZ9|TRUA_ECO7I RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226708653|sp|B7N5T0|TRUA_ECOLU RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226708654|sp|B1LLS3|TRUA_ECOSM RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238057729|sp|B5YXV8|TRUA_ECO5E RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254789635|sp|B7LBH2|TRUA_ECO55 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|12516677|gb|AAG57447.1|AE005463_10 pseudouridylate synthase I [Escherichia coli O157:H7 str. EDL933]
 gi|26109112|gb|AAN81315.1|AE016763_274 tRNA pseudouridine synthase A [Escherichia coli CFT073]
 gi|13362672|dbj|BAB36625.1| pseudouridylate synthase I [Escherichia coli O157:H7 str. Sakai]
 gi|81241877|gb|ABB62587.1| pseudouridylate synthase I [Shigella dysenteriae Sd197]
 gi|170517806|gb|ACB15984.1| tRNA pseudouridine synthase A [Escherichia coli SMS-3-5]
 gi|187771144|gb|EDU34988.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4196]
 gi|188017261|gb|EDU55383.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4113]
 gi|189001906|gb|EDU70892.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4076]
 gi|189357607|gb|EDU76026.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4401]
 gi|189362830|gb|EDU81249.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4486]
 gi|189368293|gb|EDU86709.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4501]
 gi|189372810|gb|EDU91226.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC869]
 gi|189378874|gb|EDU97290.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC508]
 gi|208727696|gb|EDZ77297.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4206]
 gi|208733139|gb|EDZ81826.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741667|gb|EDZ89349.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4042]
 gi|209158676|gb|ACI36109.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC4115]
 gi|209764788|gb|ACI80706.1| pseudouridylate synthase I [Escherichia coli]
 gi|209764790|gb|ACI80707.1| pseudouridylate synthase I [Escherichia coli]
 gi|209764792|gb|ACI80708.1| pseudouridylate synthase I [Escherichia coli]
 gi|209764796|gb|ACI80710.1| pseudouridylate synthase I [Escherichia coli]
 gi|217319539|gb|EEC27964.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           TW14588]
 gi|218352649|emb|CAU98430.1| pseudouridylate synthase I [Escherichia coli 55989]
 gi|218370780|emb|CAR18593.1| pseudouridylate synthase I [Escherichia coli IAI39]
 gi|218432945|emb|CAR13839.1| pseudouridylate synthase I [Escherichia coli UMN026]
 gi|222034074|emb|CAP76815.1| tRNA pseudouridine synthase A [Escherichia coli LF82]
 gi|227835728|gb|EEJ46194.1| tRNA pseudouridine synthase A [Escherichia coli 83972]
 gi|254593611|gb|ACT72972.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           TW14359]
 gi|284922306|emb|CBG35391.1| tRNA pseudouridine synthase A [Escherichia coli 042]
 gi|290763432|gb|ADD57393.1| tRNA pseudouridine synthase A [Escherichia coli O55:H7 str. CB9615]
 gi|291323485|gb|EFE62913.1| tRNA pseudouridine synthase A [Escherichia coli B088]
 gi|291427992|gb|EFF01019.1| tRNA pseudouridine synthase A [Escherichia coli FVEC1412]
 gi|291433259|gb|EFF06238.1| tRNA pseudouridine synthase A [Escherichia coli B185]
 gi|291471143|gb|EFF13627.1| tRNA pseudouridine synthase A [Escherichia coli B354]
 gi|298278909|gb|EFI20423.1| tRNA pseudouridine synthase A [Escherichia coli FVEC1302]
 gi|300299124|gb|EFJ55509.1| tRNA pseudouridine synthase A [Escherichia coli MS 185-1]
 gi|300396694|gb|EFJ80232.1| tRNA pseudouridine synthase A [Escherichia coli MS 69-1]
 gi|300408504|gb|EFJ92042.1| tRNA pseudouridine synthase A [Escherichia coli MS 45-1]
 gi|300458008|gb|EFK21501.1| tRNA pseudouridine synthase A [Escherichia coli MS 21-1]
 gi|300525323|gb|EFK46392.1| tRNA pseudouridine synthase A [Escherichia coli MS 119-7]
 gi|300841394|gb|EFK69154.1| tRNA pseudouridine synthase A [Escherichia coli MS 124-1]
 gi|306908627|gb|EFN39124.1| tRNA pseudouridine synthase A [Escherichia coli W]
 gi|307554380|gb|ADN47155.1| tRNA pseudouridine synthase A [Escherichia coli ABU 83972]
 gi|308123487|gb|EFO60749.1| tRNA pseudouridine synthase A [Escherichia coli MS 145-7]
 gi|308927342|gb|EFP72816.1| tRNA pseudouridine synthase A [Shigella dysenteriae 1617]
 gi|312946937|gb|ADR27764.1| tRNA pseudouridine synthase A [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315061611|gb|ADT75938.1| pseudouridylate synthase I [Escherichia coli W]
 gi|315255255|gb|EFU35223.1| tRNA pseudouridine synthase A [Escherichia coli MS 85-1]
 gi|315292275|gb|EFU51627.1| tRNA pseudouridine synthase A [Escherichia coli MS 153-1]
 gi|320192058|gb|EFW66703.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           EC1212]
 gi|320641146|gb|EFX10625.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. G5101]
 gi|320646361|gb|EFX15284.1| tRNA pseudouridine synthase A [Escherichia coli O157:H- str.
           493-89]
 gi|320651631|gb|EFX20011.1| tRNA pseudouridine synthase A [Escherichia coli O157:H- str. H
           2687]
 gi|320657383|gb|EFX25185.1| tRNA pseudouridine synthase A [Escherichia coli O55:H7 str. 3256-97
           TW 07815]
 gi|320662918|gb|EFX30242.1| tRNA pseudouridine synthase A [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320667662|gb|EFX34573.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323184362|gb|EFZ69738.1| tRNA pseudouridine synthase A [Escherichia coli 1357]
 gi|323377808|gb|ADX50076.1| tRNA pseudouridine synthase A [Escherichia coli KO11]
 gi|323944831|gb|EGB40897.1| tRNA pseudouridine synthase A [Escherichia coli H120]
 gi|326339671|gb|EGD63482.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. 1125]
 gi|326344133|gb|EGD67894.1| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. 1044]
 gi|331059634|gb|EGI31611.1| tRNA pseudouridine synthase A [Escherichia coli TA143]
 gi|331064211|gb|EGI36122.1| tRNA pseudouridine synthase A [Escherichia coli TA271]
 gi|331069093|gb|EGI40485.1| tRNA pseudouridine synthase A [Escherichia coli TA280]
 gi|331074724|gb|EGI46044.1| tRNA pseudouridine synthase A [Escherichia coli H591]
          Length = 270

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|24113690|ref|NP_708200.1| tRNA pseudouridine synthase A [Shigella flexneri 2a str. 301]
 gi|30063744|ref|NP_837915.1| tRNA pseudouridine synthase A [Shigella flexneri 2a str. 2457T]
 gi|110806283|ref|YP_689803.1| tRNA pseudouridine synthase A [Shigella flexneri 5 str. 8401]
 gi|187733598|ref|YP_001881140.1| tRNA pseudouridine synthase A [Shigella boydii CDC 3083-94]
 gi|191168731|ref|ZP_03030509.1| tRNA pseudouridine synthase A [Escherichia coli B7A]
 gi|193062289|ref|ZP_03043384.1| tRNA pseudouridine synthase A [Escherichia coli E22]
 gi|194432876|ref|ZP_03065160.1| tRNA pseudouridine synthase A [Shigella dysenteriae 1012]
 gi|209919818|ref|YP_002293902.1| tRNA pseudouridine synthase A [Escherichia coli SE11]
 gi|218554873|ref|YP_002387786.1| tRNA pseudouridine synthase A [Escherichia coli IAI1]
 gi|256017524|ref|ZP_05431389.1| tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|260844905|ref|YP_003222683.1| pseudouridylate synthase I [Escherichia coli O103:H2 str. 12009]
 gi|300818078|ref|ZP_07098290.1| tRNA pseudouridine synthase A [Escherichia coli MS 107-1]
 gi|300918510|ref|ZP_07135103.1| tRNA pseudouridine synthase A [Escherichia coli MS 115-1]
 gi|300924588|ref|ZP_07140550.1| tRNA pseudouridine synthase A [Escherichia coli MS 182-1]
 gi|301328823|ref|ZP_07221865.1| tRNA pseudouridine synthase A [Escherichia coli MS 78-1]
 gi|331653762|ref|ZP_08354763.1| tRNA pseudouridine synthase A [Escherichia coli M718]
 gi|332278531|ref|ZP_08390944.1| tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|42559800|sp|Q83QR3|TRUA_SHIFL RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|122957319|sp|Q0T2G7|TRUA_SHIF8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226708652|sp|B7M6J9|TRUA_ECO8A RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238057730|sp|B6I4U6|TRUA_ECOSE RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238691701|sp|B2TWA0|TRUA_SHIB3 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|24052758|gb|AAN43907.1| pseudouridylate synthase I [Shigella flexneri 2a str. 301]
 gi|30041999|gb|AAP17725.1| pseudouridylate synthase I [Shigella flexneri 2a str. 2457T]
 gi|110615831|gb|ABF04498.1| pseudouridylate synthase I [Shigella flexneri 5 str. 8401]
 gi|187430590|gb|ACD09864.1| tRNA pseudouridine synthase A [Shigella boydii CDC 3083-94]
 gi|190901221|gb|EDV60992.1| tRNA pseudouridine synthase A [Escherichia coli B7A]
 gi|192931955|gb|EDV84554.1| tRNA pseudouridine synthase A [Escherichia coli E22]
 gi|194418864|gb|EDX34949.1| tRNA pseudouridine synthase A [Shigella dysenteriae 1012]
 gi|209913077|dbj|BAG78151.1| tRNA pseudouridine synthase A [Escherichia coli SE11]
 gi|218361641|emb|CAQ99237.1| pseudouridylate synthase I [Escherichia coli IAI1]
 gi|257760052|dbj|BAI31549.1| pseudouridylate synthase I [Escherichia coli O103:H2 str. 12009]
 gi|281601759|gb|ADA74743.1| tRNA pseudouridine synthase A [Shigella flexneri 2002017]
 gi|300414324|gb|EFJ97634.1| tRNA pseudouridine synthase A [Escherichia coli MS 115-1]
 gi|300419219|gb|EFK02530.1| tRNA pseudouridine synthase A [Escherichia coli MS 182-1]
 gi|300529222|gb|EFK50284.1| tRNA pseudouridine synthase A [Escherichia coli MS 107-1]
 gi|300844772|gb|EFK72532.1| tRNA pseudouridine synthase A [Escherichia coli MS 78-1]
 gi|313651142|gb|EFS15541.1| tRNA pseudouridine synthase A [Shigella flexneri 2a str. 2457T]
 gi|320178707|gb|EFW53670.1| tRNA pseudouridine synthase A [Shigella boydii ATCC 9905]
 gi|320199909|gb|EFW74498.1| tRNA pseudouridine synthase A [Escherichia coli EC4100B]
 gi|323172001|gb|EFZ57645.1| tRNA pseudouridine synthase A [Escherichia coli LT-68]
 gi|324020840|gb|EGB90059.1| tRNA pseudouridine synthase A [Escherichia coli MS 117-3]
 gi|324117804|gb|EGC11703.1| tRNA pseudouridine synthase A [Escherichia coli E1167]
 gi|331048611|gb|EGI20687.1| tRNA pseudouridine synthase A [Escherichia coli M718]
 gi|332088449|gb|EGI93567.1| tRNA pseudouridine synthase A [Shigella boydii 5216-82]
 gi|332090156|gb|EGI95255.1| tRNA pseudouridine synthase A [Shigella dysenteriae 155-74]
 gi|332100883|gb|EGJ04229.1| tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|332754968|gb|EGJ85333.1| tRNA pseudouridine synthase A [Shigella flexneri 4343-70]
 gi|332755368|gb|EGJ85732.1| tRNA pseudouridine synthase A [Shigella flexneri K-671]
 gi|332756607|gb|EGJ86958.1| tRNA pseudouridine synthase A [Shigella flexneri 2747-71]
 gi|332766138|gb|EGJ96348.1| tRNA pseudouridine synthase A [Shigella flexneri 2930-71]
 gi|333001463|gb|EGK21031.1| tRNA pseudouridine synthase A [Shigella flexneri VA-6]
 gi|333001944|gb|EGK21510.1| tRNA pseudouridine synthase A [Shigella flexneri K-218]
 gi|333002687|gb|EGK22247.1| tRNA pseudouridine synthase A [Shigella flexneri K-272]
 gi|333016355|gb|EGK35686.1| tRNA pseudouridine synthase A [Shigella flexneri K-304]
 gi|333016571|gb|EGK35901.1| tRNA pseudouridine synthase A [Shigella flexneri K-227]
          Length = 270

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|325127315|gb|EGC50250.1| tRNA pseudouridine synthase A [Neisseria meningitidis N1568]
          Length = 265

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 134/245 (54%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAVRPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIGQMRQAAALLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSS 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|300897000|ref|ZP_07115479.1| tRNA pseudouridine synthase A [Escherichia coli MS 198-1]
 gi|300359181|gb|EFJ75051.1| tRNA pseudouridine synthase A [Escherichia coli MS 198-1]
          Length = 270

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|260769069|ref|ZP_05878003.1| tRNA pseudouridine synthase A [Vibrio furnissii CIP 102972]
 gi|260617099|gb|EEX42284.1| tRNA pseudouridine synthase A [Vibrio furnissii CIP 102972]
 gi|315180810|gb|ADT87724.1| tRNA pseudouridine synthase A [Vibrio furnissii NCTC 11218]
          Length = 264

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 133/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+  +S+Q  +EKA+ ++    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTQYYGWQRQREVNSVQEELEKALSVIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            HFD        ++   + A   +   I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTA--TRKMIAWTMGANANLPKNIAVRWAKEVPDEFHARFSATARRYRYVIYNHMF 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD   M  A Q L+G +DFT+FR++HCQ+ SP R I H +V   
Sbjct: 119 RPGILATGVS-HYHGELDVARMHQAGQFLLGENDFTSFRAVHCQSRSPWRNIMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I + A +F+H  +R+  GSL  VG G+     ++  L+A+DRK  G  A  EGLY
Sbjct: 178 ERYVVIDIKANAFVHHMVRNITGSLIAVGRGEQEPEWIQWLLEAKDRKLAGATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVDVDY 243


>gi|323967759|gb|EGB63171.1| tRNA pseudouridine synthase A [Escherichia coli M863]
 gi|327252589|gb|EGE64248.1| tRNA pseudouridine synthase A [Escherichia coli STEC_7v]
          Length = 270

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|209764794|gb|ACI80709.1| pseudouridylate synthase I [Escherichia coli]
          Length = 270

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNYRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|85059597|ref|YP_455299.1| tRNA pseudouridine synthase A [Sodalis glossinidius str.
           'morsitans']
 gi|84780117|dbj|BAE74894.1| pseudouridylate synthase I [Sodalis glossinidius str. 'morsitans']
          Length = 271

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+  +S+Q  +E+A+  V  E V V+ AGRTD+GVHA  QV
Sbjct: 10  MKLALGIEYDGSAYYGWQRQQEVASVQACLERALSTVADETVTVYCAGRTDAGVHATGQV 69

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +NA L     I++  ++ V   FHARFSA  R Y Y I     
Sbjct: 70  VHFDTRSRRPDTAWTLGVNANLPAD--IAVRWVAPVTDDFHARFSATARRYRYIIYNHPL 127

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD  +M  A Q L+G +DFT+FR++ CQ+ SP R + H  V   
Sbjct: 128 RPALLGRGLTHYY-HPLDAPSMARAGQCLLGENDFTSFRALQCQSRSPWRNVHHLYVTRQ 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + + + A +F+H  +R+ VGSL  VG G    + +   L  +DR + G  A  EGLY
Sbjct: 187 GRYVVVDIKANAFVHHMVRNIVGSLLEVGCGNRPESWIADLLACRDRTQAGATARAEGLY 246

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 247 LVAVDY 252


>gi|88860431|ref|ZP_01135069.1| tRNA pseudouridine synthase A [Pseudoalteromonas tunicata D2]
 gi|88817629|gb|EAR27446.1| tRNA pseudouridine synthase A [Pseudoalteromonas tunicata D2]
          Length = 262

 Score =  161 bits (407), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 140/247 (56%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ N  S+Q  +E+A+  +    V V  AGRTDSGVH   QV
Sbjct: 1   MRIALGIEYDGSNYFGWQRQNNVISVQQEVEQALSRICNHPVEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             +N+ L   D +++     V   FHARFSA  R Y Y I+ +  
Sbjct: 61  VHFDTDANRDISAFYLGMNSVLP--DAVAVRWAQEVSLDFHARFSATARRYRYVILNQNN 118

Query: 122 -PLALEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P  L+ G + + +P  LD + M  A  +L+G +DFT+FR++HCQ+++P R I H  V+ 
Sbjct: 119 RPGILKNGISHYHLP--LDADAMNQACSYLLGENDFTSFRAVHCQSNTPFRNIMHLRVDR 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
           FG+ + I + A +FLH  +R+  G L  +G GK+ ++ ++  L+ +DR +    A   GL
Sbjct: 177 FGDYVVIDIKANAFLHHMVRNITGCLIDIGIGKYPASWMKDVLELKDRTKASATAKAAGL 236

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 237 YLVDVDY 243


>gi|121728128|ref|ZP_01681164.1| tRNA pseudouridine synthase A [Vibrio cholerae V52]
 gi|229512439|ref|ZP_04401912.1| tRNA pseudouridine synthase A [Vibrio cholerae TMA 21]
 gi|121629596|gb|EAX62018.1| tRNA pseudouridine synthase A [Vibrio cholerae V52]
 gi|229350520|gb|EEO15467.1| tRNA pseudouridine synthase A [Vibrio cholerae TMA 21]
          Length = 264

 Score =  161 bits (407), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 95/246 (38%), Positives = 132/246 (53%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGLY
Sbjct: 178 SRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 238 LVSVDY 243


>gi|291548427|emb|CBL21535.1| pseudouridylate synthase I [Ruminococcus sp. SR1/5]
          Length = 245

 Score =  161 bits (407), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG +IQG +   +  + GE +   GA RTD+GVHAL  
Sbjct: 1   MKRVGLVVAYDGTKYSGWQTQPNGITIQGVLNDTLSELLGEKIETIGASRTDAGVHALGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD            ALN   ++ + I I     V+  FH R+    ++Y YRI+ R+
Sbjct: 61  VAVFDTESRIPGEKFSYALNQ--RLPEDIRIQLSEEVEPDFHPRYCDSEKTYEYRILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  E+  ++     LD + M+ A  +L+GRHDF +F     Q  + IRT+   DV   
Sbjct: 119 FPVPTERLYSYFYHYKLDVDKMKEATSYLIGRHDFASFCGSGAQVKTTIRTVTSMDVWRD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++ IR+    FL+  +R   G+L  +G+G++    ++K L+A DR   GP AP +GL 
Sbjct: 179 GDMVTIRISGTGFLYNMVRIISGTLIEIGNGQYPPERMDKILKACDRGAAGPTAPAQGLT 238

Query: 241 FDSVEY 246
              +E+
Sbjct: 239 LMGIEF 244


>gi|328958698|ref|YP_004376084.1| tRNA pseudouridine synthase A [Carnobacterium sp. 17-4]
 gi|328675022|gb|AEB31068.1| tRNA pseudouridine synthase A [Carnobacterium sp. 17-4]
          Length = 279

 Score =  161 bits (407), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 87/249 (34%), Positives = 143/249 (57%), Gaps = 5/249 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI-VVVHGAGRTDSGVHALRQ 60
           IRY +I++Y+G+ + G+Q Q +  ++QG I+KA+ ++T  I V++HG+GRTDSGVHA  Q
Sbjct: 4   IRYKLIVQYDGTHFAGFQIQPHDRTVQGEIQKALKIMTKGIEVIIHGSGRTDSGVHAKGQ 63

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD         + +ALN+    SD I + ++SIV+ +FHAR++   + Y YR+   +
Sbjct: 64  VIHFDYPFVIPAKNMKRALNSL--TSDEIFVKDVSIVEDEFHARYNTSGKKYQYRVDLNE 121

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV--N 178
            P   ++      P  LD + ++ A + L G HDF +F + H    + +RT+    V  +
Sbjct: 122 IPDPFKRLYTLHHPYPLDMDKLKNALKDLEGEHDFASFCASHSGRENKVRTVYEASVVKD 181

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
            F N +        FL+  +R FVG+L  + +G   + ++++ L+ +DR E GP A P+G
Sbjct: 182 DFNNELLFTFRGNGFLYNMVRIFVGTLLQIANGLRPADEIQRLLEVKDRNEAGPTAKPQG 241

Query: 239 LYFDSVEYS 247
           LY   V Y 
Sbjct: 242 LYLMEVYYK 250


>gi|193068139|ref|ZP_03049103.1| tRNA pseudouridine synthase A [Escherichia coli E110019]
 gi|192958418|gb|EDV88857.1| tRNA pseudouridine synthase A [Escherichia coli E110019]
          Length = 270

 Score =  161 bits (407), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPDSWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|292492023|ref|YP_003527462.1| tRNA pseudouridine synthase A [Nitrosococcus halophilus Nc4]
 gi|291580618|gb|ADE15075.1| tRNA pseudouridine synthase A [Nitrosococcus halophilus Nc4]
          Length = 259

 Score =  161 bits (407), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 89/250 (35%), Positives = 130/250 (52%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R    +EY GS + GWQ Q+   ++Q ++E+A+  V  + + V  AGRTD+GVHA  QV
Sbjct: 1   MRIAFGVEYEGSSFCGWQSQRGVPTVQATLEEAVSKVANQPITVITAGRTDAGVHAAAQV 60

Query: 62  AHFD-----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD     L   W+           + +   + +L    VD+ FHARFSA+ R Y Y I
Sbjct: 61  VHFDTTASRLEHNWI-------FGCNMNLPPEVVVLWAQPVDETFHARFSAVARHYRYVI 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
           + R+   A+   R       L    MR    HL+G HDF++FR+  CQA SPIR +   +
Sbjct: 114 LNRRVRPAIANRRVTWYCHPLSVSRMREGGAHLIGEHDFSSFRAKACQAKSPIRNVHRLE 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V    + + I + A +FLH  +R+  G L  VG G+     +E+ LQA+ R      A P
Sbjct: 174 VRRQEDFVVIDISANAFLHHMVRNIAGVLMAVGKGEQPPCWVEEVLQARCRALGSVTARP 233

Query: 237 EGLYFDSVEY 246
           +GLY   V+Y
Sbjct: 234 DGLYLMGVDY 243


>gi|261211961|ref|ZP_05926247.1| tRNA pseudouridine synthase A [Vibrio sp. RC341]
 gi|260838569|gb|EEX65220.1| tRNA pseudouridine synthase A [Vibrio sp. RC341]
          Length = 264

 Score =  161 bits (407), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 95/246 (38%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     I++   S V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWASSVPDDFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +    + LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVSHYHCE-LDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNLMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY
Sbjct: 178 GRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVEVDY 243


>gi|229591618|ref|YP_002873737.1| tRNA pseudouridine synthase A [Pseudomonas fluorescens SBW25]
 gi|229363484|emb|CAY50706.1| pseudouridylate synthase I [Pseudomonas fluorescens SBW25]
          Length = 284

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 136/251 (54%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++EKA+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYRGWQRQASGVLTVQETLEKALSKVADSPVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTQAERSMKAWV-------MGANINLPHDVSVSWAKVMPAHFHARFKAIARRYRYVI 130

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AAQHLVG HDF+ FR+  CQA SPI+ + H 
Sbjct: 131 YNDQIRPAHLNEEITW-NHRPLDAERMAEAAQHLVGVHDFSAFRAGQCQAKSPIKEVHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I + + A +FLH  +R+  G L  +G G+      ++ L+++ R+  G  A 
Sbjct: 190 RVTRHGKMIVLDIRAGAFLHHMVRNIAGVLMTIGTGERPVAWAKEVLESRVRRTGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PFGLYLVDVEY 260


>gi|312796827|ref|YP_004029749.1| tRNA pseudouridine synthase A [Burkholderia rhizoxinica HKI 454]
 gi|312168602|emb|CBW75605.1| tRNA pseudouridine synthase A (EC 4.2.1.70) [Burkholderia
           rhizoxinica HKI 454]
          Length = 271

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 135/246 (54%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + ++Y+G+ + GWQ Q +G+++Q  +E+A+       +    AGRTD+GVHAL QV
Sbjct: 6   MRIALGLQYDGAAFCGWQAQPHGNTVQNVLERALEQFAQVPLPTVVAGRTDTGVHALGQV 65

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD + +       + +NA+L  S  +S+     V   FHARF+A  R+Y Y +     
Sbjct: 66  VHFDTLLDRAAFSWVRGVNAFLPPS--VSVQWAKPVPPTFHARFAAFERTYFYVLYVHPV 123

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +   RA  +   LD E MR AA +L+G HDF++FRS  CQA +P++ +   D+   G
Sbjct: 124 RSPMLARRAGWVHTPLDVEAMREAAGYLIGEHDFSSFRSSDCQAKTPVKHLYAIDIVEHG 183

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + +R  A +FLH  +R+ +G L  VG  +  +  + + L A++RK   P   P+GLY 
Sbjct: 184 PFVHLRFRANAFLHHMVRNIMGCLVSVGRHRHPACWMAEVLAARERKHAAPTFMPDGLYL 243

Query: 242 DSVEYS 247
             V Y 
Sbjct: 244 AQVGYP 249


>gi|145299467|ref|YP_001142308.1| tRNA pseudouridine synthase A [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|166228677|sp|A4SNT8|TRUA_AERS4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|142852239|gb|ABO90560.1| tRNA pseudouridine synthase A [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 269

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 95/245 (38%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS YFGWQRQ+   S+Q  +EKA+  +    V +  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGSRYFGWQRQREVISVQAELEKALSRIANHPVSIQCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD             LN+ L     I++  +  VD+ FHARFSA  R Y Y I     
Sbjct: 61  IHFDTHAIRSESAWTLGLNSNLP--PDIAVRWVKEVDETFHARFSATARRYRYVIYNHNY 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+         +++D   M +A Q L+G  DFT+FR+I CQ+ +P R + H  V+  G
Sbjct: 119 RPAILGSGVSHYHETIDAALMHLAGQCLLGEQDFTSFRAIGCQSKTPWRNVTHLCVSRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +FLH  +R+  GSL LVG G      + + L A+DR + GP A   GLY 
Sbjct: 179 PYIVLDIRANAFLHHMVRNITGSLLLVGQGLKPVEWIAELLAAKDRNQAGPTAKAGGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|262402660|ref|ZP_06079221.1| tRNA pseudouridine synthase A [Vibrio sp. RC586]
 gi|262351442|gb|EEZ00575.1| tRNA pseudouridine synthase A [Vibrio sp. RC586]
          Length = 264

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 133/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     I++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY
Sbjct: 178 GRYVVIDLKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVDVDY 243


>gi|240000017|ref|ZP_04719941.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae 35/02]
 gi|268595826|ref|ZP_06129993.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae 35/02]
 gi|268549215|gb|EEZ44633.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae 35/02]
          Length = 265

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 133/245 (54%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+          + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDITAARPQQAWVRGVNAHLP--EGIAVLHARQVAPGFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA  LVG  DF++FR+  CQA SP++TI    +    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAALLVGEQDFSSFRAAGCQAKSPVKTIYRTGLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|212712250|ref|ZP_03320378.1| hypothetical protein PROVALCAL_03336 [Providencia alcalifaciens DSM
           30120]
 gi|212684996|gb|EEB44524.1| hypothetical protein PROVALCAL_03336 [Providencia alcalifaciens DSM
           30120]
          Length = 271

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 135/246 (54%), Gaps = 6/246 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEYNGS Y+GWQRQ+   S+QG +E A+  +  E + V+ AGRTD+GVHA  QV 
Sbjct: 9   RIALGIEYNGSRYYGWQRQQEVQSVQGCLEAALSKIAAEPISVNCAGRTDAGVHATGQVV 68

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQA 121
           HF+              N +L   D I++     VD +FHARFSA  R Y Y I   R  
Sbjct: 69  HFETSAIRKEAAWTMGTNTHL--PDDIAVRWCKPVDDEFHARFSATARRYRYVIFNHRYR 126

Query: 122 PLALEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
           P  L  G   +  P  LD + M  AAQ L+G  DFT+FR++ CQ+ +P R + H +V   
Sbjct: 127 PAILSNGVTHFHFP--LDEKRMHQAAQALLGERDFTSFRAVQCQSKTPWRNVMHVNVTRH 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           GN + + + A +F+H  +R+ VGSL  +G G      +   L+ +DR +    A  EGLY
Sbjct: 185 GNYVVVDIKANAFVHHMVRNIVGSLLEIGCGNQDIDWMAHLLELKDRTKAAATAKAEGLY 244

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 245 LVSVDY 250


>gi|121635695|ref|YP_975940.1| tRNA pseudouridine synthase A [Neisseria meningitidis FAM18]
 gi|166228740|sp|A1KWB6|TRUA_NEIMF RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|120867401|emb|CAM11173.1| tRNA pseudouridine synthase [Neisseria meningitidis FAM18]
 gi|325143594|gb|EGC65914.1| tRNA pseudouridine synthase A [Neisseria meningitidis M01-240013]
          Length = 265

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 134/245 (54%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESVPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIGPMRRAAALLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSS 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|259047524|ref|ZP_05737925.1| tRNA pseudouridine synthase A [Granulicatella adiacens ATCC 49175]
 gi|259035715|gb|EEW36970.1| tRNA pseudouridine synthase A [Granulicatella adiacens ATCC 49175]
          Length = 249

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 135/247 (54%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALR 59
           M RY + I+Y+G+ Y G+Q Q+NG+SIQ  + KA+  +T G+ + V G+GRTDSGVHA  
Sbjct: 1   MQRYKLTIQYDGTPYVGFQVQENGNSIQAELNKALKKMTKGQYIPVSGSGRTDSGVHANG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV H D  +      L +A+N+ L  S  I I++   V ++FHAR+S   + Y+Y++ T 
Sbjct: 61  QVVHIDYPKRIEANSLVRAMNSLLPTS--IRIVSAEAVSEEFHARYSVTGKRYIYKVTTA 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q      +      P   D + +  A + ++G HDFT+F S      S +R +   +V  
Sbjct: 119 QVQSPFLRQYELHHPFKTDVDRINKAFEAVIGEHDFTSFCSTKSDKDSKVRVVTKAEVKR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ +      + FL+  +R  VG+   +GDG     ++++ L+A DR   GP AP  GL
Sbjct: 179 NGDELIFTFEGKGFLYNMVRILVGTALQIGDGLREVEEMKQILEAMDRNAAGPTAPSHGL 238

Query: 240 YFDSVEY 246
           Y D V Y
Sbjct: 239 YLDEVFY 245


>gi|91211615|ref|YP_541601.1| tRNA pseudouridine synthase A [Escherichia coli UTI89]
 gi|110642522|ref|YP_670252.1| tRNA pseudouridine synthase A [Escherichia coli 536]
 gi|117624508|ref|YP_853421.1| tRNA pseudouridine synthase A [Escherichia coli APEC O1]
 gi|157155365|ref|YP_001463662.1| tRNA pseudouridine synthase A [Escherichia coli E24377A]
 gi|191170294|ref|ZP_03031848.1| tRNA pseudouridine synthase A [Escherichia coli F11]
 gi|215487531|ref|YP_002329962.1| tRNA pseudouridine synthase A [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218559231|ref|YP_002392144.1| tRNA pseudouridine synthase A [Escherichia coli S88]
 gi|218690478|ref|YP_002398690.1| tRNA pseudouridine synthase A [Escherichia coli ED1a]
 gi|237704797|ref|ZP_04535278.1| tRNA pseudouridylate synthase I [Escherichia sp. 3_2_53FAA]
 gi|300928489|ref|ZP_07144015.1| tRNA pseudouridine synthase A [Escherichia coli MS 187-1]
 gi|300986858|ref|ZP_07177840.1| tRNA pseudouridine synthase A [Escherichia coli MS 200-1]
 gi|306814570|ref|ZP_07448732.1| tRNA pseudouridine synthase A [Escherichia coli NC101]
 gi|312967618|ref|ZP_07781833.1| tRNA pseudouridine synthase A [Escherichia coli 2362-75]
 gi|331647974|ref|ZP_08349066.1| tRNA pseudouridine synthase A [Escherichia coli M605]
 gi|331658401|ref|ZP_08359363.1| tRNA pseudouridine synthase A [Escherichia coli TA206]
 gi|331683990|ref|ZP_08384586.1| tRNA pseudouridine synthase A [Escherichia coli H299]
 gi|123049014|sp|Q0TFC8|TRUA_ECOL5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|123084414|sp|Q1R994|TRUA_ECOUT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166228696|sp|A1ADG7|TRUA_ECOK1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|166991161|sp|A7ZPD3|TRUA_ECO24 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226708650|sp|B7MG82|TRUA_ECO45 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254789634|sp|B7UFX6|TRUA_ECO27 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254789636|sp|B7MXZ5|TRUA_ECO81 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|91073189|gb|ABE08070.1| tRNA pseudouridylate synthase I [Escherichia coli UTI89]
 gi|110344114|gb|ABG70351.1| tRNA pseudouridine synthase A [Escherichia coli 536]
 gi|115513632|gb|ABJ01707.1| tRNA pseudouridine synthase A [Escherichia coli APEC O1]
 gi|157077395|gb|ABV17103.1| tRNA pseudouridine synthase A [Escherichia coli E24377A]
 gi|190909810|gb|EDV69395.1| tRNA pseudouridine synthase A [Escherichia coli F11]
 gi|215265603|emb|CAS10006.1| pseudouridylate synthase I [Escherichia coli O127:H6 str. E2348/69]
 gi|218366000|emb|CAR03744.1| pseudouridylate synthase I [Escherichia coli S88]
 gi|218428042|emb|CAR08961.2| pseudouridylate synthase I [Escherichia coli ED1a]
 gi|226901163|gb|EEH87422.1| tRNA pseudouridylate synthase I [Escherichia sp. 3_2_53FAA]
 gi|281179405|dbj|BAI55735.1| tRNA pseudouridine synthase A [Escherichia coli SE15]
 gi|294491901|gb|ADE90657.1| tRNA pseudouridine synthase A [Escherichia coli IHE3034]
 gi|300306347|gb|EFJ60867.1| tRNA pseudouridine synthase A [Escherichia coli MS 200-1]
 gi|300463484|gb|EFK26977.1| tRNA pseudouridine synthase A [Escherichia coli MS 187-1]
 gi|305851964|gb|EFM52416.1| tRNA pseudouridine synthase A [Escherichia coli NC101]
 gi|307626145|gb|ADN70449.1| tRNA pseudouridine synthase A [Escherichia coli UM146]
 gi|312287815|gb|EFR15720.1| tRNA pseudouridine synthase A [Escherichia coli 2362-75]
 gi|315288292|gb|EFU47691.1| tRNA pseudouridine synthase A [Escherichia coli MS 110-3]
 gi|315298147|gb|EFU57411.1| tRNA pseudouridine synthase A [Escherichia coli MS 16-3]
 gi|320196186|gb|EFW70810.1| tRNA pseudouridine synthase A [Escherichia coli WV_060327]
 gi|323187957|gb|EFZ73252.1| tRNA pseudouridine synthase A [Escherichia coli RN587/1]
 gi|323952111|gb|EGB47985.1| tRNA pseudouridine synthase A [Escherichia coli H252]
 gi|323955889|gb|EGB51643.1| tRNA pseudouridine synthase A [Escherichia coli H263]
 gi|324009238|gb|EGB78457.1| tRNA pseudouridine synthase A [Escherichia coli MS 57-2]
 gi|331043698|gb|EGI15836.1| tRNA pseudouridine synthase A [Escherichia coli M605]
 gi|331056649|gb|EGI28658.1| tRNA pseudouridine synthase A [Escherichia coli TA206]
 gi|331078942|gb|EGI50144.1| tRNA pseudouridine synthase A [Escherichia coli H299]
          Length = 270

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSRYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|169634476|ref|YP_001708212.1| tRNA pseudouridine synthase A [Acinetobacter baumannii SDF]
 gi|260556213|ref|ZP_05828432.1| tRNA pseudouridine synthase A [Acinetobacter baumannii ATCC 19606]
 gi|238688125|sp|B0VLA5|TRUA_ACIBS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|169153268|emb|CAP02373.1| tRNA-pseudouridine synthase I [Acinetobacter baumannii]
 gi|260410268|gb|EEX03567.1| tRNA pseudouridine synthase A [Acinetobacter baumannii ATCC 19606]
          Length = 265

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 135/253 (53%), Gaps = 13/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIERVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       + A  ++   ISI  +  +D++FHARF A  R Y Y
Sbjct: 61  MVAHFDTNAIRPERGWI-------MGANSQLPKDISIQWIKQMDEEFHARFKATARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H
Sbjct: 114 VVYNAPHRPALLHKQVTHIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DRK  G  A
Sbjct: 174 CRLFEHGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDTMFAAEDRKAAGITA 233

Query: 235 PPEGLYFDSVEYS 247
           PP+GLYF    Y 
Sbjct: 234 PPDGLYFIQCYYP 246


>gi|239500845|ref|ZP_04660155.1| tRNA pseudouridine synthase A [Acinetobacter baumannii AB900]
          Length = 265

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 135/253 (53%), Gaps = 13/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIERVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       + A  ++   ISI  +  +D++FHARF A  R Y Y
Sbjct: 61  MVAHFDTNAIRQERGWI-------MGANSQLPKDISIQWIKQMDEEFHARFKATARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H
Sbjct: 114 VVYNAPHRPALLHKQVTHIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DRK  G  A
Sbjct: 174 CRLFEHGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDTMFAAEDRKAAGITA 233

Query: 235 PPEGLYFDSVEYS 247
           PP+GLYF    Y 
Sbjct: 234 PPDGLYFIQCYYP 246


>gi|324015393|gb|EGB84612.1| tRNA pseudouridine synthase A [Escherichia coli MS 60-1]
          Length = 270

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSRYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAGLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|322831951|ref|YP_004211978.1| tRNA pseudouridine synthase A [Rahnella sp. Y9602]
 gi|321167152|gb|ADW72851.1| tRNA pseudouridine synthase A [Rahnella sp. Y9602]
          Length = 276

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 92/247 (37%), Positives = 135/247 (54%), Gaps = 8/247 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + IEY+GS YFGWQRQ+  +S+Q  +EKA+  V    +VV  AGRTD+GV A  QV 
Sbjct: 17  RVALGIEYDGSAYFGWQRQQGVASVQECLEKALSRVANAPIVVFCAGRTDAGVSATGQVV 76

Query: 63  HFDLVREWVPVILCKA---LNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           HFD      PV+   A   +     +   I++   + V + FHARFSA  R Y Y I   
Sbjct: 77  HFD-----TPVLRKDAAWTMGVNTHLPKDIAVRWCANVGEDFHARFSATARRYRYVIYNN 131

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +   A+       +   LD E M++A Q L+G +DFT+FR+  CQ+ +P R + H +V+ 
Sbjct: 132 RYRSAILHAGVTHVHMPLDVEKMQLAGQALLGENDFTSFRASQCQSRTPWRYVMHVNVSR 191

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + + + A +F+H  +R+ VGSL  +G G      + + L A+DR        PEGL
Sbjct: 192 HGSYVVVDIKANAFVHHMVRNIVGSLVEIGAGNQPVGWMGELLAAKDRNLAAATGKPEGL 251

Query: 240 YFDSVEY 246
           Y   V+Y
Sbjct: 252 YLVCVDY 258


>gi|284009291|emb|CBA76427.1| tRNA pseudouridine synthase A [Arsenophonus nasoniae]
          Length = 270

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + IEY+GS Y+GWQRQ+   SIQ  +E A+  V  E + V  AGRTD+GVHA  Q
Sbjct: 9   MFKIALGIEYDGSHYYGWQRQQQVKSIQACVESALTKVAHESIQVCCAGRTDAGVHATGQ 68

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+             +N++L     I++     V+  FHARFSA  R Y Y I   +
Sbjct: 69  VIHFETSVIRKDSAWTMGVNSHLPAD--IAVRWSKDVEPDFHARFSATARRYRYIIFNHR 126

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+           LD E M IAAQ LVG  DFT+FR+I CQ+ SP R I H  VN +
Sbjct: 127 YRPAILAAGVTHYHAPLDAEKMHIAAQALVGEQDFTSFRAIQCQSKSPWRNIKHVHVNRY 186

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I + + A +F+H  +R+ VGSL  +G G      + + L  +DR +    A  EGLY
Sbjct: 187 GDYIVVDIKANAFVHHMVRNIVGSLLAIGCGVQDINWIAELLALKDRTKAAATAKAEGLY 246

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 247 LVAVDY 252


>gi|262165233|ref|ZP_06032970.1| tRNA pseudouridine synthase A [Vibrio mimicus VM223]
 gi|262024949|gb|EEY43617.1| tRNA pseudouridine synthase A [Vibrio mimicus VM223]
          Length = 264

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 133/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    + V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPIEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     +++   + V   FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDVAVRWATAVPDDFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L+ ++R      A  EGLY
Sbjct: 178 GRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLEQKNRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVEVDY 243


>gi|238685503|sp|A3M1T4|TRUA_ACIBT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|193076245|gb|ABO10878.2| tRNA-pseudouridine synthase I [Acinetobacter baumannii ATCC 17978]
          Length = 265

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 135/253 (53%), Gaps = 13/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE+ +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIERVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       + A  ++   ISI  +  +D++FHARF A  R Y Y
Sbjct: 61  MVAHFDTNAIRPERGWI-------MGANSQLPKDISIQWIKQMDEEFHARFKATARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H
Sbjct: 114 VVYNAPHRPALLHKQVTHIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DRK  G  A
Sbjct: 174 CRLFEHGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDAMFAAEDRKAAGITA 233

Query: 235 PPEGLYFDSVEYS 247
           PP+GLYF    Y 
Sbjct: 234 PPDGLYFIQCYYP 246


>gi|325199128|gb|ADY94584.1| tRNA pseudouridine synthase A [Neisseria meningitidis G2136]
          Length = 265

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 135/245 (55%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAVRPQQAWIRGVNAHLP--EGIAVLHARQVALEFHARFDAYGRHYRYLLESSPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA +L+G  DF++FR+  CQA SPI+TI   ++    
Sbjct: 126 RSPLLKNRAGWTHLKLDIGPMRQAATYLIGEQDFSSFRAAECQAKSPIKTIYRANLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|170760365|ref|YP_001787307.1| tRNA pseudouridine synthase A [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169407354|gb|ACA55765.1| tRNA pseudouridine synthase A [Clostridium botulinum A3 str. Loch
           Maree]
          Length = 246

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+TGE + +  +GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIASGRTDTGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTTFQGSTDEILNYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ IP++LD   M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHIPETLDINAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +++  +   FLH  IR   G+L  VG     S D++  L+ +DR++ GP AP +GL
Sbjct: 179 KDGYVDLVYLGSGFLHKMIRILTGTLIEVGLHNLKSVDVKNILEVEDRRKAGPTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV+Y
Sbjct: 239 FMTSVDY 245


>gi|116051110|ref|YP_790059.1| tRNA pseudouridine synthase A [Pseudomonas aeruginosa UCBPP-PA14]
 gi|115586331|gb|ABJ12346.1| tRNA-pseudouridine synthase I [Pseudomonas aeruginosa UCBPP-PA14]
          Length = 285

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 103/249 (41%), Positives = 135/249 (54%), Gaps = 9/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + IEY GS Y GWQRQ+ G  S+Q ++E+A+  V  E V V  AGRTD+ VHA  QV
Sbjct: 19  RIALGIEYKGSRYRGWQRQEAGVPSVQEALERALSKVAAEPVGVICAGRTDAAVHASGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT--- 118
            HFD   E          NA L     IS+    ++   FHARFSA+ R Y Y I     
Sbjct: 79  VHFDTAVERPLKAWVMGTNANLPAD--ISVTWARVMPAHFHARFSAMARRYRYAIYNDPI 136

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R A LA E    W   + LD   MR AAQ LVG HDFT+FR++ CQA SP++T+ H  + 
Sbjct: 137 RPAHLAEEV--TWNH-RPLDIGRMREAAQVLVGTHDFTSFRAVQCQAKSPVKTMHHVRLL 193

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G LI + +   +FLH  +R+  G L  +G G+      ++ L+ +DR+  G  A P G
Sbjct: 194 EHGRLIVLDIRGNAFLHHMVRNIAGVLMTIGAGERPIEWAKEVLETRDRRAGGVTAHPYG 253

Query: 239 LYFDSVEYS 247
           LY   VEY 
Sbjct: 254 LYLVRVEYP 262


>gi|15807281|ref|NP_296011.1| pseudouridylate synthase I [Deinococcus radiodurans R1]
 gi|42559894|sp|Q9RS37|TRUA_DEIRA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|6460099|gb|AAF11837.1|AE002061_4 pseudouridylate synthase I [Deinococcus radiodurans R1]
          Length = 280

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 93/248 (37%), Positives = 136/248 (54%), Gaps = 7/248 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVH-GAGRTDSGVHALRQV 61
           R  + + ++G  Y GWQ Q+N  S+Q +++ A+  + GE  +    AGRTD+GVHA    
Sbjct: 17  RLRLTVAWDGRDYAGWQEQRNAVSVQETLQTALHALGGEGALRPVSAGRTDAGVHAEAMP 76

Query: 62  AHFDLVREW-VPVI-LCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            H+D+   + VP++ L +ALNA+L  S  +S+L+  +    FHARFS   R Y+YR+   
Sbjct: 77  LHWDVPTTFRVPLVQLPRALNAWLPAS--VSVLSAEVAPAGFHARFSCTERRYVYRLWVA 134

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
                L  GRA  +P  LD E M  AAQ L+G HDF  F +   + +  +R +   +V  
Sbjct: 135 PQRHPLWAGRALHVPGPLDAEAMNRAAQSLIGLHDFAAFATREDRQT--VRDLLRLEVQP 192

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G L +I V   SFL   +R  VG+L LVG GK  + ++E  L +++R   G   PP GL
Sbjct: 193 QGELWDIHVAGESFLRHMVRGLVGTLLLVGQGKLGAAEVEGILASRERARAGANVPPGGL 252

Query: 240 YFDSVEYS 247
           YF   EY 
Sbjct: 253 YFAGAEYG 260


>gi|229525612|ref|ZP_04415017.1| tRNA pseudouridine synthase A [Vibrio cholerae bv. albensis VL426]
 gi|229339193|gb|EEO04210.1| tRNA pseudouridine synthase A [Vibrio cholerae bv. albensis VL426]
          Length = 264

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 95/246 (38%), Positives = 132/246 (53%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EKA+  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKALSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTSAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A  EGLY
Sbjct: 178 SRYVVIDIKANAFVHHMVRNITGSLIAVGRGEQKPEWIQWLLAQKDRTLAAATAKAEGLY 237

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 238 LVSVDY 243


>gi|240143728|ref|ZP_04742329.1| tRNA pseudouridine synthase A [Roseburia intestinalis L1-82]
 gi|257204287|gb|EEV02572.1| tRNA pseudouridine synthase A [Roseburia intestinalis L1-82]
 gi|291537295|emb|CBL10407.1| pseudouridylate synthase I [Roseburia intestinalis M50/1]
 gi|291539242|emb|CBL12353.1| pseudouridylate synthase I [Roseburia intestinalis XB6B4]
          Length = 251

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 132/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M  Y MI++Y+G+ Y GWQ      +IQG ++  +  + G  V V G+GRTD+GVHA  Q
Sbjct: 1   MANYKMILQYDGTRYRGWQVLPAELTIQGKLQDVLSKMAGYQVEVTGSGRTDAGVHAKGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
            A+F L  EW    +   LN YL   + I++  +  VD++FH+R+ A+ ++YLYRI T +
Sbjct: 61  TANFHLREEWDEDKILFYLNQYL--PEDIAVCEVKRVDERFHSRYQAVEKTYLYRIHTGK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P   E+   +   + LD   MR AA++L G HDF +F        S +RTI    +   
Sbjct: 119 IPEVFERRYVYDYTEPLDVNRMRKAAEYLCGTHDFKSFCGNKKMKKSTVRTISRIQIKEL 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
              I+I      FL   +R   G+L  +GDG+ T  D+ + L+A++R+  G  AP  GL 
Sbjct: 179 PGEIQIYYTGNGFLQNMVRILTGTLIEIGDGRRTPEDVSEILEAKNRERAGYTAPACGLT 238

Query: 241 FDSVEYS 247
              V Y 
Sbjct: 239 LLEVIYG 245


>gi|332524310|ref|ZP_08400532.1| tRNA pseudouridine synthase A [Rubrivivax benzoatilyticus JA2]
 gi|332107641|gb|EGJ08865.1| tRNA pseudouridine synthase A [Rubrivivax benzoatilyticus JA2]
          Length = 274

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 91/244 (37%), Positives = 127/244 (52%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + I Y G+ Y GWQ Q +G ++Q  +E+A+       V    AGRTD+GVHA  QV 
Sbjct: 16  RIALGIAYRGARYHGWQSQPDGRTVQDVLERALGQFAATPVGTLCAGRTDAGVHAFNQVV 75

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HFD   E       +  N YL   D +++     VD +FHAR SA  R Y + I+     
Sbjct: 76  HFDAPVERDEFSWVRGTNRYLP--DDVAVQWCRRVDARFHARNSAQGRRYRFVILEAPVR 133

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+E G    + + LD + MR AA HL+G HDF++FR+  CQA +P++T+    V   G 
Sbjct: 134 PAIEAGACGWVFRPLDGDAMRAAAAHLIGEHDFSSFRAAGCQALTPVKTMRSIGVERRGA 193

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
              I   A +FLH  +R+ VG L  VG G+     + + L A+ R    P  PP+GLYF 
Sbjct: 194 YWRIEFDASAFLHHMVRNIVGCLVTVGSGRQRPEWMAEVLAARSRDAAAPTFPPDGLYFV 253

Query: 243 SVEY 246
              Y
Sbjct: 254 GPYY 257


>gi|291618223|ref|YP_003520965.1| TruA [Pantoea ananatis LMG 20103]
 gi|291153253|gb|ADD77837.1| TruA [Pantoea ananatis LMG 20103]
 gi|327394617|dbj|BAK12039.1| tRNA pseudouridine synthase A TruA [Pantoea ananatis AJ13355]
          Length = 267

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 132/240 (55%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ+   S+Q  +E+A+  V    V V  AGRTD+GVH   QV HF+ V
Sbjct: 13  IEYDGSRYYGWQRQQEVRSVQEKLERALSKVADHPVSVFCAGRTDAGVHGTGQVVHFETV 72

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L   D I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 73  AQRADAAWTLGVNANL--PDDIAVRWVKAVPDDFHARFSATARRYRYLIYNQRLRPAILG 130

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
            G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 131 NGVTHFY-YPLDVEKMQRAGQCLLGENDFTSFRAVQCQSRTPWRNVMHLNVTRHGPYVIV 189

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  +G G  + + + + L A+DR      A  EGLY  +V+Y
Sbjct: 190 DIKANAFVHHMVRNIVGSLMEIGCGNQSESWMAELLAAKDRTLAAATAKAEGLYLVAVDY 249


>gi|168180502|ref|ZP_02615166.1| tRNA pseudouridine synthase A [Clostridium botulinum NCTC 2916]
 gi|182668817|gb|EDT80795.1| tRNA pseudouridine synthase A [Clostridium botulinum NCTC 2916]
          Length = 246

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+TGE + +  +GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTGEDINLIASGRTDTGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   V+++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTTFQGSTDEILNYCYEYL--PKDIVVYDAFHVNERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ IP++LD   M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHIPETLDINAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +++  +   FLH  IR   G+L  VG     S D++  L+A+DR++ GP AP +GL
Sbjct: 179 KDGYVDLVYLGSGFLHKMIRILTGTLIEVGLHNLKSVDVKNILKAEDRRKAGPTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV+Y
Sbjct: 239 FMTSVDY 245


>gi|49083216|gb|AAT50973.1| PA3114 [synthetic construct]
          Length = 286

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 104/249 (41%), Positives = 135/249 (54%), Gaps = 9/249 (3%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + IEY GS Y GWQRQ+ G  S+Q ++E+A   V  E V V  AGRTD+ VHA  QV
Sbjct: 19  RIALGIEYKGSRYRGWQRQEAGVPSVQEALERASSKVAAEPVGVICAGRTDAAVHASGQV 78

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT--- 118
            HFD   E          NA L     IS+    ++   FHARFSA+ R Y Y I     
Sbjct: 79  VHFDTAVERPLKAWVMGTNANLPAD--ISVTWARVMPAHFHARFSAMARRYRYAIYNDPI 136

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           R A LA E    W   + LD   MR AAQ LVG HDFT+FR++ CQA SP++T+ H  + 
Sbjct: 137 RPAHLAEEV--TWNH-RPLDIGRMREAAQVLVGTHDFTSFRAVQCQAKSPVKTMHHVRLL 193

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G LI + +   +FLH  +R+  G L  +G G+      ++ L+A+DR+  G  A P G
Sbjct: 194 EHGRLIVLDIRGNAFLHHMVRNIAGVLMTIGAGERPIEWAKEVLEARDRRAGGVTAHPYG 253

Query: 239 LYFDSVEYS 247
           LY   VEY 
Sbjct: 254 LYLVRVEYP 262


>gi|312962053|ref|ZP_07776550.1| tRNA pseudouridine synthase A [Pseudomonas fluorescens WH6]
 gi|311283863|gb|EFQ62447.1| tRNA pseudouridine synthase A [Pseudomonas fluorescens WH6]
          Length = 284

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 135/251 (53%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++EKA+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYRGWQRQASGVPTVQETLEKALSKVADSSVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTQAERTMKAWV-------MGANINLPHDVSVSWAKVMPAHFHARFKAIARRYRYVI 130

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AAQHLVG HDF+ FR+  CQA SPI+ + H 
Sbjct: 131 YNDQIRPAHLNEEITW-NHRPLDAERMAEAAQHLVGVHDFSAFRAGQCQAKSPIKEVHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I + + A +FLH  +R+  G L  +G G+       + L+++ R+  G  A 
Sbjct: 190 RVTRHGKMIVLDIRAGAFLHHMVRNIAGVLMTIGTGERPVDWAREVLESRIRRTGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PFGLYLVDVEY 260


>gi|260869040|ref|YP_003235442.1| pseudouridylate synthase I [Escherichia coli O111:H- str. 11128]
 gi|257765396|dbj|BAI36891.1| pseudouridylate synthase I [Escherichia coli O111:H- str. 11128]
 gi|323176756|gb|EFZ62346.1| tRNA pseudouridine synthase A [Escherichia coli 1180]
          Length = 270

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVMRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|119897336|ref|YP_932549.1| tRNA pseudouridine synthase A [Azoarcus sp. BH72]
 gi|119669749|emb|CAL93662.1| pseudouridine synthase A [Azoarcus sp. BH72]
          Length = 265

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 92/251 (36%), Positives = 131/251 (52%), Gaps = 12/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M+R  + +EY G  + GWQ Q++G ++Q ++E A+  + GE V +H AGRTD+GVHA  Q
Sbjct: 1   MVRLALGVEYAGDRFEGWQSQRHGRTVQDALEAALSRIAGEAVKLHCAGRTDTGVHATAQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSI-----VDKQFHARFSAIRRSYLYR 115
           VAHFD           + L+A+++  +T     +++     VD  FHARF A  R Y Y 
Sbjct: 61  VAHFD-------TAAVRPLSAWIRGVNTHLPAGVAVRWAVEVDDAFHARFLAYERRYRYV 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           +       AL  GR       LD   M  AA+ LVG  DF+ FR+  CQA +P+R +   
Sbjct: 114 LFNAPTRPALLAGRVGWFHLPLDEGAMAEAARCLVGMQDFSAFRAAECQAKTPVRDMREV 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G+ +     A  FLH  IR+ VG+L  VG G++    L + L  +DR    P   
Sbjct: 174 RVQRSGDYLIFDFRADGFLHHMIRNLVGALVYVGKGRYPPGWLAEVLAGRDRSRAAPTFA 233

Query: 236 PEGLYFDSVEY 246
           P+GLY   V Y
Sbjct: 234 PDGLYLCGVSY 244


>gi|332290494|ref|YP_004421346.1| tRNA pseudouridine synthase A [Gallibacterium anatis UMN179]
 gi|330433390|gb|AEC18449.1| tRNA pseudouridine synthase A [Gallibacterium anatis UMN179]
          Length = 265

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 89/251 (35%), Positives = 139/251 (55%), Gaps = 12/251 (4%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M +  + I Y+GS YFGWQ+Q++  SIQ  +E+A+  +  E + +  AGRTD+GVHA  Q
Sbjct: 1   MKKIALGISYDGSRYFGWQKQQSVQSIQNELEQALSTIANEPIEIFCAGRTDAGVHATGQ 60

Query: 61  VAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           V HF+      ++ W+           + + + I++   + V++ FHARFSA+ R Y Y 
Sbjct: 61  VIHFETSASRPLQAWI-------FGTNVHLPNDIAVKWSTEVNEDFHARFSALSRRYRYI 113

Query: 116 IITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
           I  R    A+           LD + M IA Q+L+G +DF++FR+  CQ+ SP R + H 
Sbjct: 114 IYNRPQRFAILPTGITHHHYPLDEKLMHIAGQYLLGENDFSSFRAAQCQSKSPYRNVHHL 173

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V+  G+ + + + A +F+H  +R+ VGSL +VG+GK     ++  LQ +DR    P A 
Sbjct: 174 QVSRIGDYLIVDIQANAFVHHMVRNIVGSLLVVGEGKQKPEWIKWLLQQRDRSCAAPTAK 233

Query: 236 PEGLYFDSVEY 246
             GLY   V Y
Sbjct: 234 AAGLYLVKVHY 244


>gi|120554480|ref|YP_958831.1| tRNA pseudouridine synthase A [Marinobacter aquaeolei VT8]
 gi|120324329|gb|ABM18644.1| tRNA pseudouridine synthase A [Marinobacter aquaeolei VT8]
          Length = 302

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 94/250 (37%), Positives = 132/250 (52%), Gaps = 13/250 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  +I EY+G  + GWQ QK+G  S++  + +A   V    V +  AGRTD+GVHA  QV
Sbjct: 18  RVAIIFEYDGQAFHGWQLQKSGVRSVEAELSRAAARVADHPVDLVCAGRTDAGVHASFQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
           AHFD      +R WV       +     + D IS+         FHARFSAI R Y Y I
Sbjct: 78  AHFDTPSVRNLRSWV-------MGMNTALPDDISVHWAGNGQGDFHARFSAIYRRYRYVI 130

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                   +++G+     + LD E M  A+Q LVG HDF++FR+  CQ+ +P+R ++   
Sbjct: 131 YNHPVRPGIQRGQVSWTFRPLDAERMHRASQALVGEHDFSSFRAAGCQSRTPVRFLEQIS 190

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V   G  + I V A +FLH  +R+  G+L  VG+G+     +   L+ +DRK  G  APP
Sbjct: 191 VTRCGEFVVIDVQANAFLHHMVRNIAGALMAVGNGQQPEDWIGDILECRDRKLAGVTAPP 250

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 251 YGLYLVDVGY 260


>gi|323161584|gb|EFZ47470.1| tRNA pseudouridine synthase A [Escherichia coli E128010]
          Length = 270

 Score =  160 bits (405), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG        + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPECWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|77358715|ref|YP_338281.1| tRNA pseudouridine synthase A [Coxiella burnetii RSA 493]
 gi|153206765|ref|ZP_01945606.1| tRNA pseudouridine synthase A [Coxiella burnetii 'MSU Goat Q177']
 gi|154705837|ref|YP_001424337.1| tRNA pseudouridine synthase A [Coxiella burnetii Dugway 5J108-111]
 gi|161830159|ref|YP_001596814.1| tRNA pseudouridine synthase A [Coxiella burnetii RSA 331]
 gi|165918506|ref|ZP_02218592.1| tRNA pseudouridine synthase A [Coxiella burnetii RSA 334]
 gi|212212657|ref|YP_002303593.1| tRNA pseudouridine synthase A [Coxiella burnetii CbuG_Q212]
 gi|212218370|ref|YP_002305157.1| tRNA pseudouridine synthase A [Coxiella burnetii CbuK_Q154]
 gi|226708643|sp|B6J6W3|TRUA_COXB1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226708644|sp|B6J0H0|TRUA_COXB2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226708645|sp|A9KFZ5|TRUA_COXBN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|226708646|sp|A9ND24|TRUA_COXBR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|71066705|gb|AAZ22627.1| tRNA pseudouridine synthase A [Coxiella burnetii RSA 493]
 gi|120577128|gb|EAX33752.1| tRNA pseudouridine synthase A [Coxiella burnetii 'MSU Goat Q177']
 gi|154355123|gb|ABS76585.1| tRNA pseudouridine synthase A [Coxiella burnetii Dugway 5J108-111]
 gi|161762026|gb|ABX77668.1| tRNA pseudouridine synthase A [Coxiella burnetii RSA 331]
 gi|165917752|gb|EDR36356.1| tRNA pseudouridine synthase A [Coxiella burnetii RSA 334]
 gi|212011067|gb|ACJ18448.1| tRNA pseudouridine synthase A [Coxiella burnetii CbuG_Q212]
 gi|212012632|gb|ACJ20012.1| tRNA pseudouridine synthase A [Coxiella burnetii CbuK_Q154]
          Length = 261

 Score =  160 bits (405), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 93/252 (36%), Positives = 133/252 (52%), Gaps = 14/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + I Y+GS Y GWQ Q+   ++QG +EKA+  V    V V  AGRTD+GVHA  Q
Sbjct: 1   MARIALGIRYDGSAYHGWQVQEALKTVQGEVEKALSAVANHPVFVTCAGRTDAGVHASAQ 60

Query: 61  VAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYR 115
           VAHFD         WV         A   +   ISIL    V++ FHAR+SA+ R Y Y 
Sbjct: 61  VAHFDTTAYRSDHAWV-------FGANSNLPHDISILWAKAVEEDFHARYSAMARRYRYI 113

Query: 116 IITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           +   +  P  L K   W   + LD + M+  AQ+L+G HDF++F+   CQ+ +P+R I  
Sbjct: 114 VYNHEIRPAILRKAIGWHY-RPLDEKRMQAGAQYLIGEHDFSSFQGAGCQSRTPVRKIFQ 172

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            ++     ++ I V A +FL   +R+  G L  +G G+      +  L+A+DR++ G   
Sbjct: 173 IEIYRIRRMVVIEVQANAFLLHMVRNIAGVLIAIGSGEKHPDWAQTVLKAKDRRQGGVTV 232

Query: 235 PPEGLYFDSVEY 246
           PP GLY   V Y
Sbjct: 233 PPNGLYLVEVNY 244


>gi|114562572|ref|YP_750085.1| tRNA pseudouridine synthase A [Shewanella frigidimarina NCIMB 400]
 gi|122300225|sp|Q084R8|TRUA_SHEFN RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|114333865|gb|ABI71247.1| tRNA pseudouridine synthase A [Shewanella frigidimarina NCIMB 400]
          Length = 261

 Score =  160 bits (405), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 127/245 (51%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+GS + GWQRQ    S+Q  IEKA+  V  E + V  AGRTD+GVH   QV
Sbjct: 1   MRVALGIEYDGSSFCGWQRQLEVDSVQAQIEKALSYVANEPITVSCAGRTDTGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +       + +NA   + D+++I     VD  FHAR+SA  R Y Y I   + 
Sbjct: 61  VHFDTDVQRPMTAWTQGVNA--NLPDSVAIRWAKEVDDSFHARYSATARRYRYVIYNHKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +           +D   M  AAQ  VG HDFT+FR++HCQ+ +P R +   +V   G
Sbjct: 119 RPGILSAGVSHYHGDIDETLMHKAAQLFVGEHDFTSFRALHCQSKTPFRNVHQVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G      + +    ++RK   P A P GLY 
Sbjct: 179 MYVMVDIQANAFLHHMVRNIVGSLLQIGLGNQPIEWITELFALKNRKLAAPTAKPNGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|74312835|ref|YP_311254.1| tRNA pseudouridine synthase A [Shigella sonnei Ss046]
 gi|123759585|sp|Q3YZP3|TRUA_SHISS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|73856312|gb|AAZ89019.1| pseudouridylate synthase I [Shigella sonnei Ss046]
 gi|323168509|gb|EFZ54189.1| tRNA pseudouridine synthase A [Shigella sonnei 53G]
          Length = 270

 Score =  160 bits (405), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG        + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPERWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|240129104|ref|ZP_04741765.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae SK-93-1035]
 gi|268687486|ref|ZP_06154348.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae SK-93-1035]
 gi|268627770|gb|EEZ60170.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae SK-93-1035]
          Length = 265

 Score =  160 bits (405), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPGFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA  L+G  DF++FR+  CQA SP++TI    +    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAALLIGEQDFSSFRAAECQAKSPVKTIYRTGLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|330837397|ref|YP_004412038.1| tRNA pseudouridine synthase A [Spirochaeta coccoides DSM 17374]
 gi|329749300|gb|AEC02656.1| tRNA pseudouridine synthase A [Spirochaeta coccoides DSM 17374]
          Length = 299

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 99/256 (38%), Positives = 141/256 (55%), Gaps = 15/256 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  M + Y+G+GY GWQ Q+N  S+Q  IE A++ +TG  V V G+GRTDSGVHAL QV 
Sbjct: 21  RVRMTVAYDGTGYSGWQHQRNAPSVQAEIEDALYRLTGHSVTVVGSGRTDSGVHALGQVC 80

Query: 63  HFDLVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
           HFDL  E  P V+  +ALNA+L  +  I I++    +  FHARFSA+ R Y Y +I R+A
Sbjct: 81  HFDLPDERFPAVVFKRALNAFLPPA--IRIMDSEETNDSFHARFSAMAREYRY-LIKREA 137

Query: 122 PLA-LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI--HCQASSPIRTIDHFDVN 178
            +   + GR W++ +    E ++  A  + G HDFTTF +    C+       +  F V 
Sbjct: 138 DMTPFDSGRVWVVKELPSLELLKAHAAEIAGTHDFTTFTAAGDMCERRHRDIYVSDFSVE 197

Query: 179 SFGNLIEIRV---VARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
              +  E+ V      +FL+  +RS VG+L  +  G   +T+  + L A+DR + G  A 
Sbjct: 198 KDIHGAEVLVYTICGNAFLYKMVRSIVGTLFFLVLGGVPATETARRLAARDRSQAGRTAS 257

Query: 236 PEGLY-----FDSVEY 246
             GLY     FD  EY
Sbjct: 258 AHGLYLSRISFDEKEY 273


>gi|194429433|ref|ZP_03061956.1| tRNA pseudouridine synthase A [Escherichia coli B171]
 gi|194412494|gb|EDX28793.1| tRNA pseudouridine synthase A [Escherichia coli B171]
 gi|195183057|dbj|BAG66617.1| pseudouridylate synthase I [Escherichia coli O111:H-]
          Length = 270

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
            +         +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AQRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG        + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPECWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|149175153|ref|ZP_01853776.1| tRNA pseudouridine synthase A [Planctomyces maris DSM 8797]
 gi|148846131|gb|EDL60471.1| tRNA pseudouridine synthase A [Planctomyces maris DSM 8797]
          Length = 267

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 97/264 (36%), Positives = 132/264 (50%), Gaps = 27/264 (10%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + + Y+GS Y GWQ Q NG S+Q  +EKAI  +T +   V  AGRTD+GVHAL QVA F 
Sbjct: 6   LTLAYDGSEYAGWQVQPNGPSVQACVEKAIEQLTQQRSPVLVAGRTDAGVHALGQVASFQ 65

Query: 66  LVREWVPVILCKALNAYLK--ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPL 123
                   I CK L   L+  + ++I +  +  V   FHA +SAI++ Y Y I     P 
Sbjct: 66  TES----AIPCKNLQTGLQRFLPESICVREVREVPPDFHATYSAIQKRYRYVIHNSAVPY 121

Query: 124 ALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-- 181
              K       + LD + M  A Q L+G+HDF  F S +   ++ +RTI    V   G  
Sbjct: 122 PFLKKYVSEFGRPLDSDRMHAAGQQLLGQHDFRCFESHYPNKATSVRTITELTVQRTGVW 181

Query: 182 -------------------NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKAL 222
                                I + VVA  FL+  +R+ VG+L  VG G+WTS D++K L
Sbjct: 182 PVWGVLEQAHLSMENSTSAEFITVDVVADGFLYNMVRAIVGTLLDVGVGRWTSNDVQKIL 241

Query: 223 QAQDRKECGPLAPPEGLYFDSVEY 246
              DR + GP AP  GLY   V+Y
Sbjct: 242 TGMDRSQAGPTAPACGLYLVQVDY 265


>gi|261868098|ref|YP_003256020.1| tRNA pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413430|gb|ACX82801.1| tRNA pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 261

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 94/252 (37%), Positives = 139/252 (55%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EY+G  YFGWQRQ+  +SIQ  +E+AI +V  E + +  AGRTDSGVHA  QV
Sbjct: 1   MKIALGVEYDGKHYFGWQRQEKVASIQAELERAISVVANEDIGIFCAGRTDSGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +NA L   D I++    +V+  FHARFSA  R Y Y       
Sbjct: 61  LHFETTAQRPEKAWSFGVNANL--PDDIAVRWAKVVEDDFHARFSATARRYRYI------ 112

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            L   K R+ ++P+        LD + M  A Q L+G +DF++FR+  CQ+++P R + H
Sbjct: 113 -LYCNKLRSAILPQGVTHYHLELDHQLMHGAGQALLGENDFSSFRAAQCQSNTPWRNVHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  I + + A +F+H  +R+ VGSL  VG G      ++  L+ +DR    P A
Sbjct: 172 LNVTRQGQYIIVDIQANAFVHHMVRNIVGSLIEVGCGNQPVEWMKWLLEQKDRTLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
            PEGLY  +V Y
Sbjct: 232 KPEGLYLVNVIY 243


>gi|124267346|ref|YP_001021350.1| tRNA pseudouridine synthase A [Methylibium petroleiphilum PM1]
 gi|166228739|sp|A2SHS6|TRUA_METPP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|124260121|gb|ABM95115.1| Pseudouridylate synthase [Methylibium petroleiphilum PM1]
          Length = 260

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 124/245 (50%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y G  Y GWQ Q +G ++Q  +E+A+       V    AGRTD+GVHAL QV
Sbjct: 1   MRLALGLSYRGGAYRGWQSQPDGLTVQDRVEEALARFADRPVRTVCAGRTDAGVHALNQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            H D   E  P    +  N YL     I++     VD  FHAR SA  R Y Y ++    
Sbjct: 61  VHLDTEIEREPFSWVRGTNRYLP--PDIAVQWCRPVDAAFHARNSARGRRYAYLLLESPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+E G    + + LD   MR AA HL+G HDF+ FRS  CQA+SP++ +   ++   G
Sbjct: 119 RPAIEAGAVGWVFRPLDATPMREAAAHLIGEHDFSAFRSAECQAASPVKNLRRIEIVRCG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                   A +FLH  +R+ +G L  VG G      L + L A DR+   P   P+GLYF
Sbjct: 179 AYWRFEFEASAFLHHMVRNLMGCLLAVGQGVRAPQWLAEVLAAGDRRRAAPTFAPDGLYF 238

Query: 242 DSVEY 246
              +Y
Sbjct: 239 LGPQY 243


>gi|192361259|ref|YP_001982227.1| tRNA pseudouridine synthase A [Cellvibrio japonicus Ueda107]
 gi|190687424|gb|ACE85102.1| tRNA pseudouridine synthase A [Cellvibrio japonicus Ueda107]
          Length = 299

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 96/253 (37%), Positives = 138/253 (54%), Gaps = 13/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + +EY G+ + G+Q Q NG  ++Q S+EKA+ +V  E + +  AGRTD+GVHA  
Sbjct: 28  MRRVALGVEYKGADFHGFQVQPNGVKTVQQSLEKALSIVADEPITLVCAGRTDAGVHATN 87

Query: 60  QVAHFDLVREWVPVILCKALNAYLK-----ISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD + +       + L A+++     + DTI I     V   FHARFSA  R+Y Y
Sbjct: 88  QVIHFDTLAQ-------RPLKAWMRGLGPHLPDTIGIRWAQDVSPGFHARFSAQSRTYRY 140

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +    +  AL   +     + LD   MR  A  L+G HDFT+FR+  CQA SP+R I++
Sbjct: 141 LMSDGASSPALLHDQVSWSSRPLDVALMRQGAACLIGEHDFTSFRATQCQAKSPVRRIEY 200

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G LI + + A +FLH  +R+ VG L  VG G    + +   L A+DR   G  A
Sbjct: 201 LHLVRRGELIVMEIRANAFLHHMVRNIVGVLMQVGAGFKKPSWVGDVLAARDRTAAGATA 260

Query: 235 PPEGLYFDSVEYS 247
            P GLY  +V+Y 
Sbjct: 261 KPNGLYLVAVDYP 273


>gi|283832251|ref|ZP_06351992.1| tRNA pseudouridine synthase A [Citrobacter youngae ATCC 29220]
 gi|291071892|gb|EFE10001.1| tRNA pseudouridine synthase A [Citrobacter youngae ATCC 29220]
          Length = 270

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 96/240 (40%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E V V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPVSVFCAGRTDAGVHGTGQVVHFETH 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  AVRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLG 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V  FG  + +
Sbjct: 134 KGVTHYY-EPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVERFGAYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|229056264|ref|ZP_04195685.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH603]
 gi|228721069|gb|EEL72607.1| tRNA pseudouridine synthase A 2 [Bacillus cereus AH603]
          Length = 268

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 138/247 (55%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ Y GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 24  MNNYKLTIQYDGARYKGWQRLGNNDNTIQGKIESIISEMVGKEIEIIGCSRTDAGVHALN 83

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI ++  V  +FHAR+++  ++YLY+I   
Sbjct: 84  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITSVEEVPDRFHARYNSKAKTYLYKIWNE 141

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   DV+ 
Sbjct: 142 EHTNPFMRKYSMHVNKQLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLDVSE 201

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+     +   L+ + R +   LA   GL
Sbjct: 202 ESGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLEVDAIPNILEEKQRNQINCLAEASGL 261

Query: 240 YFDSVEY 246
           Y + +E+
Sbjct: 262 YLEKIEF 268


>gi|240118890|ref|ZP_04732952.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID1]
 gi|240126753|ref|ZP_04739639.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae SK-92-679]
 gi|268604599|ref|ZP_06138766.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID1]
 gi|268685331|ref|ZP_06152193.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae SK-92-679]
 gi|268588730|gb|EEZ53406.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID1]
 gi|268625615|gb|EEZ58015.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae SK-92-679]
          Length = 265

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPGFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA  LVG  DF++FR+  CQA SP++TI    +    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAALLVGEQDFSSFRAAGCQAKSPVKTIYRAGLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|253996350|ref|YP_003048414.1| tRNA pseudouridine synthase A [Methylotenera mobilis JLW8]
 gi|253983029|gb|ACT47887.1| tRNA pseudouridine synthase A [Methylotenera mobilis JLW8]
          Length = 261

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 125/245 (51%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + + Y+GS Y GWQ Q +   +Q ++E A+  V    V VH AGRTD+GVHAL Q+
Sbjct: 1   MKIALGVSYDGSLYCGWQSQPSACGVQDALESALQDVAQHAVRVHAAGRTDTGVHALGQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +       + +NA+L    TI +     VD  FHARFSA  RSY Y +     
Sbjct: 61  VHFETDAKRPLSAWVRGVNAHLPA--TIRVEWAHAVDDDFHARFSAFSRSYQYLLYNAPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL   +A      LD   M  AA +L+G HDFT FR+  CQA + IR +    V   G
Sbjct: 119 ASALMADKAGWFHLPLDYAAMSEAASYLIGEHDFTAFRASECQAKTAIRHMSQAGVVQSG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                   A +FL  Q+R+ VG+L  +G GK+    + + LQ +DR    P   P GLY 
Sbjct: 179 QFFLFNFSANAFLQHQVRNMVGALIYIGKGKYPPAYMRELLQGKDRTLSPPTFSPNGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 TDVGY 243


>gi|259907892|ref|YP_002648248.1| tRNA pseudouridine synthase A [Erwinia pyrifoliae Ep1/96]
 gi|224963514|emb|CAX55004.1| tRNA pseudouridylate synthase I [Erwinia pyrifoliae Ep1/96]
 gi|283477767|emb|CAY73683.1| pseudouridylate synthase I [Erwinia pyrifoliae DSM 12163]
          Length = 271

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 90/239 (37%), Positives = 130/239 (54%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V    + V  AGRTD+GVH   QV HF+  
Sbjct: 17  IEYDGSRYYGWQRQNEVRSVQEKLEKALAKVADRPIAVFCAGRTDAGVHGTGQVVHFETT 76

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
            +         +NA L     I++  +  V   FHARFSA  R Y Y I  ++   A+  
Sbjct: 77  AQRKDAAWTLGVNANLPAD--IAVRWVKAVADDFHARFSATARRYRYVIYNQRLRPAILA 134

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
           G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P+R + H  V+  G  + + 
Sbjct: 135 GGVTHFYHPLDVEKMQRAGQCLLGENDFTSFRAVQCQSRTPMRNVMHLKVSRHGAYVVVD 194

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A +F+H  +R+ VGSL  +G G      + + L A+DRK     A  EGLY  +V+Y
Sbjct: 195 IKANAFVHHMVRNIVGSLMEIGCGNQPEGWMRELLVAKDRKLAAATARAEGLYLVAVDY 253


>gi|271501293|ref|YP_003334318.1| tRNA pseudouridine synthase A [Dickeya dadantii Ech586]
 gi|270344848|gb|ACZ77613.1| tRNA pseudouridine synthase A [Dickeya dadantii Ech586]
          Length = 292

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 136/247 (55%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ    S+QG +E A+  V  E + V  AGRTD+GVHA  QV
Sbjct: 13  LKIALGIEYDGSRYYGWQRQAEVGSVQGCLEAALSQVANERIDVFCAGRTDAGVHATGQV 72

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            HF              +NA L     I++  +  VD+ FHARFSA  R Y Y I  R+ 
Sbjct: 73  VHFTTNAVRKDAAWTMGVNANLPPD--IAVRWVKTVDEAFHARFSATARRYRYVIYNRRF 130

Query: 121 APLALEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P  L  G   + +P  LD + M  A Q L+G +DFT+FR++ CQ+ +P R + H  V  
Sbjct: 131 RPAILSHGVTHYYLP--LDADRMHRAGQCLLGENDFTSFRAVQCQSRTPWRNLMHLRVTR 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + + + A +F+H  +R+ VGSL  +G G      +++ L A+DR      A  +GL
Sbjct: 189 LGDYVVVDIKANAFVHHMVRNIVGSLMEIGCGNQPENWMDELLAAKDRTLAAATAKADGL 248

Query: 240 YFDSVEY 246
           Y  +V+Y
Sbjct: 249 YLVAVDY 255


>gi|304311263|ref|YP_003810861.1| tRNA pseudouridine synthase A [gamma proteobacterium HdN1]
 gi|301796996|emb|CBL45209.1| tRNA pseudouridine synthase A [gamma proteobacterium HdN1]
          Length = 265

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 101/246 (41%), Positives = 129/246 (52%), Gaps = 3/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           +R  + IEY+GS Y GWQRQ +  +++Q  +E A+  V    V V   GRTD+GVH   Q
Sbjct: 1   MRIALGIEYDGSPYHGWQRQGHEPNTVQQILESALSQVADHPVTVICCGRTDAGVHGYGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HFD      P       NA L  S  IS+     V + FHARFSA  R Y Y I    
Sbjct: 61  VVHFDTHAMRTPRAWIHGANAALPHS--ISVRWSQEVPEHFHARFSAYARRYCYVIYNHP 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              AL         + LD   M   AQ LVG HDFT+FR++ CQA SPI+TI    V   
Sbjct: 119 IRPALGMRHMTWQYRPLDERQMEEGAQALVGTHDFTSFRALGCQAKSPIKTIHSIRVERR 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G +I I V A ++LH  +R+  G L  VG GK  S  +++ L+ +DR   G  APP GLY
Sbjct: 179 GAMIFISVHANAYLHHMVRNIAGVLMAVGTGKAASRWVKEVLELRDRSRGGVTAPPYGLY 238

Query: 241 FDSVEY 246
           F   +Y
Sbjct: 239 FMEAQY 244


>gi|325141434|gb|EGC63912.1| tRNA pseudouridine synthase A [Neisseria meningitidis 961-5945]
          Length = 265

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 134/245 (54%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q +G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQADGVPTVQAALETALAQIAGEAVSTIVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V  +FHARF A  R Y Y + +   
Sbjct: 68  VHFDTAAARPQQAWVRGVNAHLP--EGIAVLHARQVAPEFHARFDAYGRHYRYLLESVPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  L+G  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIGPMRRAAALLIGEQDFSSFRAAECQAKSPVKTIYRADLTQSS 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|310768198|gb|ADP13148.1| tRNA pseudouridine synthase A [Erwinia sp. Ejp617]
          Length = 271

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 90/239 (37%), Positives = 131/239 (54%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V    + V  AGRTD+GVH   QV HF+  
Sbjct: 17  IEYDGSRYYGWQRQNEVRSVQEKLEKALAKVADRPIAVFCAGRTDAGVHGTGQVVHFETT 76

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
            +         +NA L     I++  +  V   FHARFSA  R Y Y I  ++   A+  
Sbjct: 77  AQRKDAAWTLGVNANLPAD--IAVRWVKAVADDFHARFSATARRYRYVIYNQRLRPAILA 134

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
           G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P+R + H +V+  G  + + 
Sbjct: 135 GGVTHFYHPLDVEKMQRAGQCLLGENDFTSFRAVQCQSRTPMRNVMHLNVSRHGAYVVVD 194

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A +F+H  +R+ VGSL  +G G      + + L A+DRK     A  EGLY  +V+Y
Sbjct: 195 IKANAFVHHMVRNIVGSLIEIGCGNQPEGWMRELLVAKDRKLAAATARAEGLYLVAVDY 253


>gi|187478755|ref|YP_786779.1| tRNA pseudouridine synthase A [Bordetella avium 197N]
 gi|123738625|sp|Q2KYM0|TRUA_BORA1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|115423341|emb|CAJ49875.1| tRNA pseudouridine synthase A [Bordetella avium 197N]
          Length = 267

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 94/253 (37%), Positives = 140/253 (55%), Gaps = 14/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +G ++Q ++E A+  F  TG  +    AGRTD+GVHA 
Sbjct: 1   MTRIALGLSYDGSSWQGWQTQPHGQTVQDTLEAALGQFSGTGAPLDTLCAGRTDTGVHAA 60

Query: 59  RQVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            QV H D         WV     + +NA+L  S  ISI     V + FHARFSA  R+Y+
Sbjct: 61  MQVVHVDTHLNRRAESWV-----RGVNAFLPSS--ISIHWAKEVGEDFHARFSARSRTYV 113

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y +   +   AL   RA    + LD   MR AAQ L+G HDF++FRS  CQA  P+R + 
Sbjct: 114 YLLWRGRVRPALWAHRAGWCFQPLDVTAMRQAAQALLGEHDFSSFRSSQCQARHPVRHLT 173

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             D+   G+ +   + A +FLH  +R+ +G+L  +G G+ +   +   L+A+DR+   P 
Sbjct: 174 RLDIAERGSFLVFTLQANAFLHHMVRNIMGALLQIGQGRESVDWMASLLRARDRRLGAPT 233

Query: 234 APPEGLYFDSVEY 246
             P+GLY  +++Y
Sbjct: 234 FSPDGLYLSAIDY 246


>gi|323483257|ref|ZP_08088647.1| tRNA pseudouridine synthase A [Clostridium symbiosum WAL-14163]
 gi|323691247|ref|ZP_08105522.1| pseudouridylate synthase [Clostridium symbiosum WAL-14673]
 gi|323403355|gb|EGA95663.1| tRNA pseudouridine synthase A [Clostridium symbiosum WAL-14163]
 gi|323504587|gb|EGB20374.1| pseudouridylate synthase [Clostridium symbiosum WAL-14673]
          Length = 341

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 92/247 (37%), Positives = 133/247 (53%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ Y GWQ Q NG +I+  + KA+  +  E V V GA RTDSGVHA   
Sbjct: 1   MKRIKLTVAYDGTAYCGWQIQPNGVTIEEVLNKALTGLLKEPVTVIGASRTDSGVHARGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +C ALN   ++ D I +     V   FH R +   ++Y Y+I+ R+
Sbjct: 61  VAVFDTESRIPGDKICFALNQ--RLPDDIRVQASEEVPLSFHPRKANCTKTYEYKILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             + LE+  +     +LD E M+ AA  LVG HDF +F ++  QA   +RTI   DV+  
Sbjct: 119 ISMPLERLYSHFCYFNLDVEKMKQAAAFLVGEHDFKSFCTVRTQAEETVRTIYSLDVSKD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G++I IR+    FL+  +R   G+L  VG G +    +E+ L+A+DR   GP  P  GL 
Sbjct: 179 GDMITIRISGSGFLYNMVRIITGTLVKVGLGVYPPEHMEEILEARDRSAAGPTIPAVGLT 238

Query: 241 FDSVEYS 247
             S+EY 
Sbjct: 239 LVSLEYE 245


>gi|325523908|gb|EGD02125.1| tRNA pseudouridine synthase A [Burkholderia sp. TJI49]
          Length = 270

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + I+Y+G+ + GWQ Q +G ++Q ++E A+       +    AGRTD+GVH L QV
Sbjct: 1   MRIALGIQYDGAAFCGWQAQPHGKTVQNALEHALAEFARVPLHTTVAGRTDTGVHGLGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +  P    +  NA+L  S  +++     +   FHARFSA  R+Y Y +     
Sbjct: 61  VHFDTDLDREPFSWVRGTNAFLPPS--VAVQWAKPMPDAFHARFSAFERTYYYALYVHPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +   RA  I   LD + MR AA HL+G HDF++FRS  CQ+ +P++ +   D+   G
Sbjct: 119 RSPMLDRRAGWIHTPLDDDAMRTAAAHLIGEHDFSSFRSSECQSKTPVKHLYQIDIRRVG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + +  R  A +FLH  +R+ +G L  VG G++ +  +   L  +DR    P    +GLY 
Sbjct: 179 HFLHFRFRANAFLHHMVRNLMGCLVAVGRGRYPADWMAAVLAGRDRNLAAPTFMADGLYL 238

Query: 242 DSVEYS 247
             V Y 
Sbjct: 239 AHVGYP 244


>gi|320174675|gb|EFW49808.1| tRNA pseudouridine synthase A [Shigella dysenteriae CDC 74-1112]
          Length = 270

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  VPRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|320540467|ref|ZP_08040117.1| pseudouridylate synthase I [Serratia symbiotica str. Tucson]
 gi|320029398|gb|EFW11427.1| pseudouridylate synthase I [Serratia symbiotica str. Tucson]
          Length = 273

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 96/240 (40%), Positives = 131/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQ+Q+  +S+QG +E+A+  V    + V  AGRTDSGVHA  QV HF+  
Sbjct: 18  IEYDGSRYYGWQQQREVASVQGCLEQALSKVADAPINVLCAGRTDSGVHATGQVVHFETS 77

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +N +L     I++  +S V   FHARFSAI R Y Y I   R  P  L+
Sbjct: 78  ARRKDAAWSMGVNTHL--PPDIAVRWVSAVADDFHARFSAIARRYRYIIYNHRNRPAVLQ 135

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           +G        LD   M  AAQ L+G +DFT+FR+  CQ+ +P R + H  V   G  I +
Sbjct: 136 QGVTHFY-HPLDAVRMHRAAQALLGENDFTSFRAAQCQSRTPWRKVKHVKVTRQGEYIVV 194

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  +G GK     L + L  +DR      A  EGLY  SV+Y
Sbjct: 195 DIKANAFVHHMVRNIVGSLMEIGCGKRNENWLAELLALRDRNLAAATARAEGLYLVSVDY 254


>gi|229171272|ref|ZP_04298862.1| tRNA pseudouridine synthase A 2 [Bacillus cereus MM3]
 gi|228612229|gb|EEK69461.1| tRNA pseudouridine synthase A 2 [Bacillus cereus MM3]
          Length = 250

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMIGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN +L   + ISI N+  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQHL--PNDISITNVEEVQDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYSLEVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDADAIPNILEEKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|260439477|ref|ZP_05793293.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae DGI2]
 gi|291042704|ref|ZP_06568449.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae DGI2]
 gi|291013373|gb|EFE05335.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae DGI2]
          Length = 265

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPGFHARFDASGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA  LVG  DF++FR+  CQA SP++TI    +    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAASLLVGEQDFSSFRAAGCQAKSPVKTIYRTGLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|225573074|ref|ZP_03781829.1| hypothetical protein RUMHYD_01265 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039560|gb|EEG49806.1| hypothetical protein RUMHYD_01265 [Blautia hydrogenotrophica DSM
           10507]
          Length = 245

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 84/247 (34%), Positives = 135/247 (54%), Gaps = 2/247 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +I+ Y+G+ Y GWQ Q NG +IQG + + +  + GE +   GA RTD+GVHA+  
Sbjct: 1   MKRVGLIVAYDGTNYCGWQVQPNGITIQGELNRCLSELLGEEIETIGASRTDAGVHAMGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  ALN   ++ + I I     +   FH R+    ++Y YRI+ R+
Sbjct: 61  VAVFDTETRMPGEKISYALNQ--RLPEDIRIQLSEEMPMDFHPRYCDSVKTYEYRILNRR 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
             +  E+  ++     LD + MR A  +L+GRHDF +F     Q  S +RTI   +V  F
Sbjct: 119 FQIPTERLYSYFYHYKLDEKKMREATSYLIGRHDFASFCGAGAQVKSTVRTIRSVEVERF 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++ IR+    FL+  +R   G+L  +G+G++    +++ L A+DR+  GP AP +GL 
Sbjct: 179 GDMVTIRISGEGFLYNMVRIIAGTLIEIGNGQYPPERMQEILDARDREWAGPTAPAKGLT 238

Query: 241 FDSVEYS 247
              ++Y 
Sbjct: 239 LLGIQYE 245


>gi|90579292|ref|ZP_01235102.1| tRNA pseudouridine synthase A [Vibrio angustum S14]
 gi|90440125|gb|EAS65306.1| tRNA pseudouridine synthase A [Vibrio angustum S14]
          Length = 261

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G+ Y+GWQRQ++  S+Q  +EKA+  V  + V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGVEYDGAKYYGWQRQRDVDSVQERLEKALSKVANQPVEVFCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+  +   V      NA+L     I++   + V + FHARF+A  R Y Y I     
Sbjct: 61  VHFDINIDRKMVAWTMGANAHL--PKDIAVRWATEVSEDFHARFTATARRYRYIIFNNAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q+L+G +DFT+FR++HCQ+ SP R + H  V   G
Sbjct: 119 RPAILGNGVSHYHGHLDEKKMHEAGQYLLGENDFTSFRAVHCQSRSPWRNLMHLKVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  VG G+     +E  L  ++R   G  A  EGLY 
Sbjct: 179 DFVIIDIKANAFVHHMVRNITGSLIKVGKGEENPEWIEWLLAQKNRTLAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|240081654|ref|ZP_04726197.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae FA19]
 gi|268597753|ref|ZP_06131920.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae FA19]
 gi|268551541|gb|EEZ46560.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae FA19]
          Length = 265

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDTAAVRPAQAWVRGVNAHLP--EGIAVLHARQVAPGFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA  LVG  DF++FR+  CQA SP++TI    +    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAALLVGEQDFSSFRAAGCQAKSPVKTIYRTGLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|304411873|ref|ZP_07393484.1| tRNA pseudouridine synthase A [Shewanella baltica OS183]
 gi|307303359|ref|ZP_07583114.1| tRNA pseudouridine synthase A [Shewanella baltica BA175]
 gi|304349733|gb|EFM14140.1| tRNA pseudouridine synthase A [Shewanella baltica OS183]
 gi|306913719|gb|EFN44141.1| tRNA pseudouridine synthase A [Shewanella baltica BA175]
          Length = 261

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+GYFGWQRQ    S+Q  +E+A+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGNGYFGWQRQAEVDSVQAQLERALSIVANEPIGVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA   + D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETHAIRNEGAWTLGVNA--NLPDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         +D + M  AAQ L+G  DFT+FR++ CQ+ +P R I   +V   G
Sbjct: 119 RPGILRHGVSHYHGDIDADRMHQAAQALLGEQDFTSFRAVQCQSKTPFRNIHCVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDIAANAFLHHMVRNIVGSLLEIGLGNQPLTWMGDLLALKDRNQAAATAKPHGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|228906232|ref|ZP_04070119.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis IBL 200]
 gi|228853388|gb|EEM98158.1| tRNA pseudouridine synthase A 2 [Bacillus thuringiensis IBL 200]
          Length = 250

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 139/247 (56%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQR-QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M  Y + I+Y+G+ + GWQR   N ++IQG IE  I  + G+ + + G  RTD+GVHAL 
Sbjct: 6   MNNYKLTIQYDGARFKGWQRLGNNDNTIQGKIESVISEMVGKEIEIIGCSRTDAGVHALN 65

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    + V   + K LN YL   + ISI ++  V  +FHAR+++  ++YLY+I   
Sbjct: 66  QVANFQSDEKLVEHKVKKYLNQYL--PNDISITSVEEVQDRFHARYNSKAKTYLYKIWNE 123

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  +  + K L+ ++M+ AA+HLVG HDFT F +   +  S +R +   +V  
Sbjct: 124 EHTNPFMRKYSMHVNKKLNVKSMKEAAKHLVGSHDFTAFSNAKSKKKSMVREVYTLEVME 183

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               ++IRV    FLH  +R  VG+L  VG G+  +  +   L+ + R +   LA   GL
Sbjct: 184 EAGFVQIRVSGNGFLHNMVRKIVGALIEVGLGQLDADAIPNILEEKQRNQINCLAEASGL 243

Query: 240 YFDSVEY 246
           Y ++VE+
Sbjct: 244 YLENVEF 250


>gi|73541994|ref|YP_296514.1| tRNA pseudouridine synthase A [Ralstonia eutropha JMP134]
 gi|123774054|sp|Q46YW3|TRUA_RALEJ RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|72119407|gb|AAZ61670.1| tRNA pseudouridine synthase [Ralstonia eutropha JMP134]
          Length = 273

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 90/250 (36%), Positives = 141/250 (56%), Gaps = 6/250 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  + + Y+G+ + GWQ Q + +++Q  +E +I    G  ++   AGRTD+GVHAL Q
Sbjct: 1   MNRIAIGLHYDGAAFSGWQSQPHRNTVQDYLEDSIERFAGVRLLTTVAGRTDAGVHALGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V H D   +       + +NA+L  S  I++     VD+ FHARF A  R Y Y + T  
Sbjct: 61  VIHLDTTLDRTTFSWVRGINAFLPPS--IALQWARPVDESFHARFLAFERMYYYALYTGP 118

Query: 121 APLALEKGRA--WLIP--KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
             + L  GRA   ++P  + LD + M+ A++ L+G  DF++FR+  CQA SP++T+    
Sbjct: 119 HRVPLAHGRAGYLMLPPGQRLDVDAMQAASRCLLGEQDFSSFRAAECQAKSPVKTMYDVT 178

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           + + GN + +R  A +FLH  +R+ +G L  VG G++    L + L A+DRK   P   P
Sbjct: 179 LKADGNWVFLRFRASAFLHHMVRNLMGCLVAVGRGRYPPEWLAEVLAARDRKLAAPTFMP 238

Query: 237 EGLYFDSVEY 246
           +GLY   V+Y
Sbjct: 239 DGLYLADVKY 248


>gi|300312591|ref|YP_003776683.1| tRNA pseudouridine synthase [Herbaspirillum seropedicae SmR1]
 gi|300075376|gb|ADJ64775.1| tRNA pseudouridine synthase protein [Herbaspirillum seropedicae
           SmR1]
          Length = 300

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 94/274 (34%), Positives = 137/274 (50%), Gaps = 32/274 (11%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + ++Y+G+ + GWQ Q +  ++Q  +E A+   + + +    AGRTDSGVHAL Q+ 
Sbjct: 13  RVVLGVQYDGASWQGWQTQPHRQTVQDQLEAALQRFSTQPIATTCAGRTDSGVHALEQIV 72

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISI---LNLSIVDKQ------------------- 100
           HFD           +  NA+L    TI++     L  VD                     
Sbjct: 73  HFDTPIARDSFSWVRGTNAFLP--PTIAVRWACELPYVDDAAIASAASQAAELHGADRAG 130

Query: 101 --------FHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGR 152
                   FHARFSAI R+Y Y +        L  G+A    + LD + M  AAQHL+G 
Sbjct: 131 ADSLSQFGFHARFSAIARTYHYVLYNHAVRTPLLAGKAGWTFRPLDADRMHRAAQHLIGE 190

Query: 153 HDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGK 212
           HDFT+FR++ CQA SP+R ++   V   G++I   + A +FLH  +R+ VGSL +VG GK
Sbjct: 191 HDFTSFRAVECQAKSPVRKMESIAVRRHGDMIVFTLKANAFLHHMVRNIVGSLVVVGSGK 250

Query: 213 WTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
                + + L  +DR    P   P+GLY   V+Y
Sbjct: 251 QEPDWMGQVLALRDRSRAAPTFMPDGLYLARVDY 284


>gi|161502487|ref|YP_001569599.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|189030140|sp|A9MJ57|TRUA_SALAR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|160863834|gb|ABX20457.1| hypothetical protein SARI_00531 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 270

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 96/240 (40%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                V     +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  ALRKDVAWTLGVNANL--PGDIAVRWVKAVADDFHARFSATARRYRYIIYNHRLRPAVLA 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      K LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   G  + +
Sbjct: 134 KGVTHYY-KPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHISVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLLEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|8569326|pdb|1DJ0|A Chain A, The Crystal Structure Of E. Coli Pseudouridine Synthase I
           At 1.5 Angstrom Resolution
 gi|8569327|pdb|1DJ0|B Chain B, The Crystal Structure Of E. Coli Pseudouridine Synthase I
           At 1.5 Angstrom Resolution
          Length = 264

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 10  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 69

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 70  ALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLS 127

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 128 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 186

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 187 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 246


>gi|240124428|ref|ZP_04737384.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID332]
 gi|268683056|ref|ZP_06149918.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID332]
 gi|268623340|gb|EEZ55740.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID332]
          Length = 265

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPGFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA  L+G  DF++FR+  CQA SP++TI    +    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAALLIGEQDFSSFRAAGCQAKSPVKTIYRAGLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|300717686|ref|YP_003742489.1| tRNA pseudouridylate synthase I [Erwinia billingiae Eb661]
 gi|299063522|emb|CAX60642.1| tRNA pseudouridylate synthase I [Erwinia billingiae Eb661]
          Length = 271

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 95/244 (38%), Positives = 134/244 (54%), Gaps = 2/244 (0%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           +  + IEY+GS Y+GWQRQ+   S+Q  +EKA+  V    V V  AGRTD+GVH   QV 
Sbjct: 12  KLALGIEYDGSHYYGWQRQQEVRSVQEKLEKALSKVADHPVSVFCAGRTDAGVHGTGQVV 71

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           HF+             +NA L   D I++  +  V   FHARFSA  R Y Y I  R+  
Sbjct: 72  HFETTSLRKDAAWTLGVNANL--PDDIAVRWVKPVSDDFHARFSATARRYRYVIYNRRLR 129

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
            A+  G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P R + H +V+ FG 
Sbjct: 130 PAILHGGVTHFYHPLDVERMQRAGQSLLGENDFTSFRAVQCQSRTPWRRVFHLNVSRFGA 189

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            + + + A +F+H  +R+ VGSL  VG G    + + + L A+DR      A  EGLY  
Sbjct: 190 YVIVDIKANAFVHHMVRNIVGSLMEVGCGNQQESWIAELLAAKDRTLAAATARAEGLYLV 249

Query: 243 SVEY 246
           SV+Y
Sbjct: 250 SVDY 253


>gi|160875946|ref|YP_001555262.1| tRNA pseudouridine synthase A [Shewanella baltica OS195]
 gi|189030142|sp|A9KTU7|TRUA_SHEB9 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|160861468|gb|ABX50002.1| tRNA pseudouridine synthase A [Shewanella baltica OS195]
 gi|315268141|gb|ADT94994.1| tRNA pseudouridine synthase A [Shewanella baltica OS678]
          Length = 261

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+GYFGWQRQ    S+Q  +E+A+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGNGYFGWQRQAEVDSVQAQLERALSIVANEPIGVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA   + D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETNAIRNEGAWTLGVNA--NLPDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         +D + M  AAQ L+G  DFT+FR++ CQ+ +P R +   +V   G
Sbjct: 119 RPGILRHGVSHYHGDIDADRMHQAAQALLGEQDFTSFRAVQCQSKTPFRNVHCVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDIAANAFLHHMVRNIVGSLLEIGLGNQPLTWMGDLLALKDRNQAAATAKPHGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|157363557|ref|YP_001470324.1| tRNA pseudouridine synthase ACD [Thermotoga lettingae TMO]
 gi|166991166|sp|A8F526|TRUA_THELT RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157314161|gb|ABV33260.1| tRNA pseudouridine synthase A [Thermotoga lettingae TMO]
          Length = 245

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 92/247 (37%), Positives = 132/247 (53%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R+  I+ Y+G+ + G+Q QK+  ++QG  E+A+  +  + V+   AGRTD+GVHA  Q
Sbjct: 1   MKRFMAIVSYDGTNFCGFQVQKDVRTVQGMFEQALERILKQRVITIAAGRTDTGVHANGQ 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           +  FD   +     +  A+NA L   D I +  +  VDK FH RF A RR Y Y I   Q
Sbjct: 61  IVCFDCYLDIDEESMKNAMNANL--PDDIYVRKVVEVDKNFHPRFDAKRRIYHYLIYNSQ 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P    +  AW  P  L+   MR AA+   G HDF +F        + +RTI    V   
Sbjct: 119 EPNLFIRNYAWWFPYKLNICKMREAAKFFEGEHDFRSFMKSGDHRENTVRTIYRVRVLQL 178

Query: 181 -GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G +I IRV  RSFL   +R+ VG+L  VG G+W   D+ + L+ +DR +    APP GL
Sbjct: 179 RGGIILIRVEGRSFLRRMVRNMVGALVKVGVGEWKPEDISRVLELKDRSKAAVTAPPHGL 238

Query: 240 YFDSVEY 246
           Y  +V++
Sbjct: 239 YLYAVDF 245


>gi|315634336|ref|ZP_07889623.1| tRNA pseudouridine synthase A [Aggregatibacter segnis ATCC 33393]
 gi|315476926|gb|EFU67671.1| tRNA pseudouridine synthase A [Aggregatibacter segnis ATCC 33393]
          Length = 261

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 95/252 (37%), Positives = 136/252 (53%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EY+G  YFGWQ+Q+  +S+Q  +E+AI  V  E + +  AGRTDSGVHA  QV
Sbjct: 1   MKIALGVEYDGKRYFGWQKQEKVASVQAELEQAISTVANEEISIFCAGRTDSGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA L   D I++    +VD  FHARFSA  R Y Y       
Sbjct: 61  IHFETTANRPEKAWSFGVNANL--PDDIAVRWAKVVDDDFHARFSATARRYRYI------ 112

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            L   K R+ ++P+        LD + M  A Q L+G +DF++FR+  CQ+++P R + H
Sbjct: 113 -LYCNKLRSAILPQGITHCHLELDHQLMHQAGQALLGENDFSSFRAAQCQSNTPWRNVHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V+  G  I + + A +F+H  +R+ VGSL  VG G      L   L  QDR    P A
Sbjct: 172 LNVSRQGQYIIVDIQANAFVHHMVRNIVGSLIEVGCGNQPVEWLAWLLGQQDRTLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
            PEGLY  +V Y
Sbjct: 232 KPEGLYLVNVLY 243


>gi|16130253|ref|NP_416821.1| pseudouridylate synthase I [Escherichia coli str. K-12 substr.
           MG1655]
 gi|89109138|ref|AP_002918.1| pseudouridylate synthase I [Escherichia coli str. K-12 substr.
           W3110]
 gi|170081934|ref|YP_001731254.1| tRNA pseudouridine synthase A [Escherichia coli str. K-12 substr.
           DH10B]
 gi|238901493|ref|YP_002927289.1| pseudouridylate synthase I [Escherichia coli BW2952]
 gi|123176|sp|P07649|TRUA_ECOLI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; Short=PSU-I; AltName:
           Full=tRNA-uridine isomerase I
 gi|229557954|sp|B1X929|TRUA_ECODH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|259550387|sp|C4ZVL1|TRUA_ECOBW RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|149242461|pdb|2NQP|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 gi|149242462|pdb|2NQP|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 gi|149242463|pdb|2NQP|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 gi|149242464|pdb|2NQP|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 gi|149242466|pdb|2NR0|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 gi|149242467|pdb|2NR0|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 gi|149242468|pdb|2NR0|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 gi|149242469|pdb|2NR0|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 gi|149242475|pdb|2NRE|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
           Complex With Leucyl Trna
 gi|41718|emb|CAA26522.1| unnamed protein product [Escherichia coli K-12]
 gi|1788657|gb|AAC75378.1| pseudouridylate synthase I [Escherichia coli str. K-12 substr.
           MG1655]
 gi|1799711|dbj|BAA16175.1| pseudouridylate synthase I [Escherichia coli str. K12 substr.
           W3110]
 gi|169889769|gb|ACB03476.1| tRNA pseudouridine synthase A [Escherichia coli str. K-12 substr.
           DH10B]
 gi|238863332|gb|ACR65330.1| pseudouridylate synthase I [Escherichia coli BW2952]
 gi|260448588|gb|ACX39010.1| tRNA pseudouridine synthase A [Escherichia coli DH1]
 gi|315136953|dbj|BAJ44112.1| tRNA pseudouridine synthase A [Escherichia coli DH1]
          Length = 270

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  ALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|293398170|ref|ZP_06642375.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae F62]
 gi|291611433|gb|EFF40503.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae F62]
          Length = 265

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPGFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E MR AA  L+G  DF++FR+  CQA SP++TI    +    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMRRAAALLIGEQDFSSFRAAGCQAKSPVKTIYRAGLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|328951248|ref|YP_004368583.1| tRNA pseudouridine synthase A [Marinithermus hydrothermalis DSM
           14884]
 gi|328451572|gb|AEB12473.1| tRNA pseudouridine synthase A [Marinithermus hydrothermalis DSM
           14884]
          Length = 249

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 92/248 (37%), Positives = 130/248 (52%), Gaps = 5/248 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + +EY+G+ + G+QRQ  G  ++Q  +E A+  + G +  V  AGRTD+GVHAL 
Sbjct: 1   MRRIKLTLEYDGTRFAGFQRQAKGERTVQAELESALAQIPGAVPKVVAAGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
            V H+D      P  +  ALN  L     +  L        FHAR+S   R Y YRI+ R
Sbjct: 61  MVVHYDTEDRIPPEKIPYALNRLL--PPDVRALAAEAAPPGFHARYSCHWRRYRYRILNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           Q P AL + R W +PK LD   M+    H +G HDF  F +   + +  +RT+    +  
Sbjct: 119 QMPSALARERTWWVPKPLDANAMQQGLAHFLGEHDFKAFATQERRGT--VRTLYRARLER 176

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  I I +V   FL  Q+R+ VG+L  VG GK     +   L   +RK+ GP APP+GL
Sbjct: 177 CGEEIVIDLVGNGFLRGQVRAMVGTLVEVGLGKRDPDVIAWLLAHGERKDAGPSAPPQGL 236

Query: 240 YFDSVEYS 247
           YF +  Y+
Sbjct: 237 YFVAAGYA 244


>gi|229844824|ref|ZP_04464962.1| tRNA pseudouridine synthase A [Haemophilus influenzae 6P18H1]
 gi|229812205|gb|EEP47896.1| tRNA pseudouridine synthase A [Haemophilus influenzae 6P18H1]
          Length = 269

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIDIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+     +        NA+L   D I++     VD +FHARFSAI R Y Y +   + 
Sbjct: 61  VHFETNAVRLEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSAIARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L G HDF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLFGEHDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L  ++R+   P A P+GLY 
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEVGAGNKPIEWMQWLLDQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|188533312|ref|YP_001907109.1| tRNA pseudouridine synthase A [Erwinia tasmaniensis Et1/99]
 gi|188028354|emb|CAO96215.1| tRNA pseudouridylate synthase I [Erwinia tasmaniensis Et1/99]
          Length = 271

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 135/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V    V V  AGRTD+GVH   QV
Sbjct: 11  VKLALGIEYDGSRYYGWQRQNEVRSVQEKLEKALAKVADCPVNVFCAGRTDAGVHGTGQV 70

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +NA L     I++  +  V  +FHARFSA  R Y Y I  ++ 
Sbjct: 71  VHFETTAQRKDAAWTLGVNANLPAD--IAVRWVKAVPDEFHARFSATARRYRYIIYNQRL 128

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M+ A Q L+G +DFT+FR++ CQ+ +P+R + H +V+  G
Sbjct: 129 RPAILAGGVTHFYHPLDVEKMQRAGQCLLGENDFTSFRAVQCQSRTPMRNVIHLNVSRHG 188

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +F+H  +R+ VGSL  +G G      + + + A+DRK     A  EGLY 
Sbjct: 189 AYVVVDIKANAFVHHMVRNIVGSLMEIGCGNQPEGWMRELMIARDRKLAAATARAEGLYL 248

Query: 242 DSVEY 246
            +V+Y
Sbjct: 249 VAVDY 253


>gi|90408620|ref|ZP_01216774.1| tRNA pseudouridine synthase A [Psychromonas sp. CNPT3]
 gi|90310264|gb|EAS38395.1| tRNA pseudouridine synthase A [Psychromonas sp. CNPT3]
          Length = 261

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 132/246 (53%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQK+  S+Q  +EKA+ +V    V V+ AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTAYYGWQRQKDVISVQEELEKALSIVANHSVRVNCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD       V     +NA L     I++     VD  FHARFSA  R Y Y I     
Sbjct: 61  IHFDTQAVRNDVAWTLGINANL--PKDIAVRWCKHVDDSFHARFSATARRYRYIIYNHVL 118

Query: 122 -PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD + M  A Q +VG HDFT+FR++HCQA++P+R+I   +V   
Sbjct: 119 RPGILNSGLSHY-HHLLDADKMHQAGQFIVGTHDFTSFRALHCQANTPVRSIHSLNVTRR 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
            + I I + A +FLH  +R+  GSL  +G        L   L+ ++R      A P GLY
Sbjct: 178 ADFIIIDIKANAFLHHMVRNIAGSLIEIGQDNQKVDWLMTLLEYKNRARAAATAKPGGLY 237

Query: 241 FDSVEY 246
              V+Y
Sbjct: 238 LVEVDY 243


>gi|126174949|ref|YP_001051098.1| tRNA pseudouridine synthase A [Shewanella baltica OS155]
 gi|166229833|sp|A3D666|TRUA_SHEB5 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|125998154|gb|ABN62229.1| tRNA pseudouridine synthase A [Shewanella baltica OS155]
          Length = 261

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+GYFGWQRQ    S+Q  +E+A+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGNGYFGWQRQAEVDSVQAQLERALSIVANEPIGVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA   + D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETQAIRNEGAWTLGVNA--NLPDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         +D + M  AAQ L+G  DFT+FR++ CQ+ +P R +   +V   G
Sbjct: 119 RPGILRHGVSHYHGDIDADRMHQAAQALLGEQDFTSFRAVQCQSKTPFRNVHCVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDIAANAFLHHMVRNIVGSLLEIGLGNQPLTWMGDLLALKDRNQAAATAKPHGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|94311405|ref|YP_584615.1| tRNA pseudouridine synthase A [Cupriavidus metallidurans CH34]
 gi|93355257|gb|ABF09346.1| pseudouridylate synthase I [Cupriavidus metallidurans CH34]
          Length = 278

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 89/248 (35%), Positives = 141/248 (56%), Gaps = 6/248 (2%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVA 62
           R  + + Y+GS Y GWQ Q + +++Q  +E AI    G  ++   AGRTD+GVHAL QV 
Sbjct: 5   RIAIGLHYDGSAYSGWQSQPHRNTVQDHLEDAIERFAGVRLLTTVAGRTDAGVHALGQVI 64

Query: 63  HFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT--RQ 120
           H D   +       + +NA+L  S  I++     VD+ FHARF A  R Y Y + T   +
Sbjct: 65  HLDTELDRDRFSWVRGVNAFLPPS--IALQWAEPVDENFHARFLAYERMYYYALYTGPHR 122

Query: 121 APLALEKGRAWLIP--KSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           AP+   +    ++P  + LD E MR A+  L+G HDF+ FR+  CQA SP++T+    + 
Sbjct: 123 APMIHGRAGYLMLPHGQRLDTEAMRRASACLLGEHDFSAFRAAECQAKSPVKTMYDVTIE 182

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
           + GN + +R  A +FLH  +R+ +G L  VG G++ +  + + L+ ++R++  P   P+G
Sbjct: 183 ADGNWVFLRFRASAFLHHMVRNLMGCLVAVGRGRYPAEWMAEVLEGRNRQKAAPTFMPDG 242

Query: 239 LYFDSVEY 246
           LY   V+Y
Sbjct: 243 LYLVDVKY 250


>gi|157161806|ref|YP_001459124.1| tRNA pseudouridine synthase A [Escherichia coli HS]
 gi|170019373|ref|YP_001724327.1| tRNA pseudouridine synthase A [Escherichia coli ATCC 8739]
 gi|188492228|ref|ZP_02999498.1| tRNA pseudouridine synthase A [Escherichia coli 53638]
 gi|194436017|ref|ZP_03068119.1| tRNA pseudouridine synthase A [Escherichia coli 101-1]
 gi|253772758|ref|YP_003035589.1| tRNA pseudouridine synthase A [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162327|ref|YP_003045435.1| tRNA pseudouridine synthase A [Escherichia coli B str. REL606]
 gi|256021997|ref|ZP_05435862.1| tRNA pseudouridine synthase A [Escherichia sp. 4_1_40B]
 gi|300948533|ref|ZP_07162627.1| tRNA pseudouridine synthase A [Escherichia coli MS 116-1]
 gi|300956414|ref|ZP_07168705.1| tRNA pseudouridine synthase A [Escherichia coli MS 175-1]
 gi|301023565|ref|ZP_07187329.1| tRNA pseudouridine synthase A [Escherichia coli MS 196-1]
 gi|301647579|ref|ZP_07247376.1| tRNA pseudouridine synthase A [Escherichia coli MS 146-1]
 gi|307138983|ref|ZP_07498339.1| tRNA pseudouridine synthase A [Escherichia coli H736]
 gi|312973422|ref|ZP_07787594.1| tRNA pseudouridine synthase A [Escherichia coli 1827-70]
 gi|331642958|ref|ZP_08344093.1| tRNA pseudouridine synthase A [Escherichia coli H736]
 gi|166991162|sp|A8A2I7|TRUA_ECOHS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030133|sp|B1IXM4|TRUA_ECOLC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157067486|gb|ABV06741.1| tRNA pseudouridine synthase A [Escherichia coli HS]
 gi|169754301|gb|ACA77000.1| tRNA pseudouridine synthase A [Escherichia coli ATCC 8739]
 gi|188487427|gb|EDU62530.1| tRNA pseudouridine synthase A [Escherichia coli 53638]
 gi|194424745|gb|EDX40730.1| tRNA pseudouridine synthase A [Escherichia coli 101-1]
 gi|242377951|emb|CAQ32720.1| tRNA pseudouridine synthase I [Escherichia coli BL21(DE3)]
 gi|253323802|gb|ACT28404.1| tRNA pseudouridine synthase A [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974228|gb|ACT39899.1| tRNA pseudouridine synthase A [Escherichia coli B str. REL606]
 gi|253978395|gb|ACT44065.1| tRNA pseudouridine synthase A [Escherichia coli BL21(DE3)]
 gi|299880800|gb|EFI89011.1| tRNA pseudouridine synthase A [Escherichia coli MS 196-1]
 gi|300316763|gb|EFJ66547.1| tRNA pseudouridine synthase A [Escherichia coli MS 175-1]
 gi|300451943|gb|EFK15563.1| tRNA pseudouridine synthase A [Escherichia coli MS 116-1]
 gi|301074269|gb|EFK89075.1| tRNA pseudouridine synthase A [Escherichia coli MS 146-1]
 gi|309702630|emb|CBJ01959.1| tRNA pseudouridine synthase A [Escherichia coli ETEC H10407]
 gi|310332017|gb|EFP99252.1| tRNA pseudouridine synthase A [Escherichia coli 1827-70]
 gi|315615587|gb|EFU96219.1| tRNA pseudouridine synthase A [Escherichia coli 3431]
 gi|323936608|gb|EGB32895.1| tRNA pseudouridine synthase A [Escherichia coli E1520]
 gi|323940985|gb|EGB37172.1| tRNA pseudouridine synthase A [Escherichia coli E482]
 gi|323961391|gb|EGB57002.1| tRNA pseudouridine synthase A [Escherichia coli H489]
 gi|323973098|gb|EGB68291.1| tRNA pseudouridine synthase A [Escherichia coli TA007]
 gi|331039756|gb|EGI11976.1| tRNA pseudouridine synthase A [Escherichia coli H736]
 gi|332344100|gb|AEE57434.1| tRNA pseudouridine synthase TruA [Escherichia coli UMNK88]
          Length = 270

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  ALRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|229846251|ref|ZP_04466363.1| tRNA pseudouridine synthase A [Haemophilus influenzae 7P49H1]
 gi|229811255|gb|EEP46972.1| tRNA pseudouridine synthase A [Haemophilus influenzae 7P49H1]
          Length = 269

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 89/250 (35%), Positives = 131/250 (52%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSCIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+       + W       A      + D I++     VD +FHARFSA  R Y Y +
Sbjct: 61  VHFETNAVRPEKAW-------AFGTNANLPDDIAVAWAKQVDDEFHARFSATARRYRYIL 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
              +   A+  G        LD E M  A Q L+G HDF++FR+  CQ+ +P R + H +
Sbjct: 114 YCNKLRSAILAGGMTHCHLDLDAEKMHQAGQCLLGEHDFSSFRAAQCQSHTPWRNVHHLN 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           V+  G  I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P
Sbjct: 174 VSRIGQYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKP 233

Query: 237 EGLYFDSVEY 246
           +GLY   V Y
Sbjct: 234 DGLYLVDVIY 243


>gi|56460125|ref|YP_155406.1| tRNA pseudouridine synthase A [Idiomarina loihiensis L2TR]
 gi|62901213|sp|Q5QUE5|TRUA_IDILO RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|56179135|gb|AAV81857.1| Pseudouridylate synthase (tRNA psi55) [Idiomarina loihiensis L2TR]
          Length = 261

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 132/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+GS Y+GWQRQ+  +S+Q  +E+A+  +    V V  AGRTD+GVHA  Q+
Sbjct: 1   MRMALCLEYDGSRYYGWQRQREVASVQQCVEEALSKIANAPVEVTCAGRTDAGVHATAQI 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+      V     +N+ L     I++     VD +F ARFSA  R Y Y I   + 
Sbjct: 61  VHFDVPVPRADVAWTLGVNSNLPAG--IAVRWAREVDSEFSARFSATSRRYRYIIANTRF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              +         + LD E M+ AAQ LVG HDFT FR+ HCQ+ +P R +    V   G
Sbjct: 119 RPGIHSAGVSHYHQPLDAEVMQEAAQALVGEHDFTAFRASHCQSHTPFRKVSDLTVERRG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + I + + A +FLH  +R+ VGSL +VG        + + L+ +DR +    A P GLY 
Sbjct: 179 DYIIVDISANAFLHHMVRNIVGSLIVVGQHLQPPDWIGELLRQKDRTKAAATAKPGGLYL 238

Query: 242 DSVEY 246
            +V Y
Sbjct: 239 VAVTY 243


>gi|297521911|ref|ZP_06940297.1| tRNA pseudouridine synthase A [Escherichia coli OP50]
          Length = 259

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 10  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 69

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 70  ALRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 127

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 128 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 186

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 187 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 246


>gi|300724021|ref|YP_003713336.1| pseudouridylate synthase I [Xenorhabdus nematophila ATCC 19061]
 gi|297630553|emb|CBJ91218.1| pseudouridylate synthase I [Xenorhabdus nematophila ATCC 19061]
          Length = 281

 Score =  159 bits (402), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 139/246 (56%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ+   S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV
Sbjct: 16  VKIALGIEYDGSRYYGWQRQQEVRSVQECLEKALSQVANEPISVFCAGRTDAGVHATGQV 75

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF+   +         +N +L     I++  +  VD +FHARFSA  R Y Y I   R 
Sbjct: 76  VHFETSAQRKDAAWTMGVNTHLP--SNIAVRWIKTVDDEFHARFSATARRYRYVIFNHRY 133

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L +G        LD + M  AAQ L+G +DFT+FR++ CQ++SP R + H +V+  
Sbjct: 134 RPAVLAQG-IMHFHSPLDEKKMHEAAQSLLGENDFTSFRAVQCQSNSPWRNMMHINVSRH 192

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ I + + A +F+H  +R+ VGSL  +G G      + + L  +DR +    A  +GLY
Sbjct: 193 GHYIVVDIKANAFVHHMVRNIVGSLLEIGCGNQNIGWMAELLTLKDRTKAAATAKADGLY 252

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 253 LVAVDY 258


>gi|309973317|gb|ADO96518.1| tRNA pseudouridine synthase A [Haemophilus influenzae R2846]
          Length = 269

 Score =  159 bits (402), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSHIANEKIDIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSAI R Y Y +   + 
Sbjct: 61  VHFETNAVRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSAIARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L G HDF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLFGEHDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEVGAGNKPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|296131870|ref|YP_003639117.1| tRNA pseudouridine synthase A [Thermincola sp. JR]
 gi|296030448|gb|ADG81216.1| tRNA pseudouridine synthase A [Thermincola potens JR]
          Length = 246

 Score =  159 bits (402), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 92/244 (37%), Positives = 136/244 (55%), Gaps = 6/244 (2%)

Query: 6   MIIEYNGSGYFGWQRQ--KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           M IEY+G+ Y G+Q+Q  +N  +IQ ++EKA+  +TGE + V GAGRTD+GVHAL QV +
Sbjct: 6   MTIEYDGTSYHGFQKQADQNLPTIQEALEKALRKLTGEEISVTGAGRTDAGVHALGQVIN 65

Query: 64  FDLVREWVPV-ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
           F      +P     +ALN+ L   + I   +       FHA+F A +++Y Y I     P
Sbjct: 66  F-YTESSIPTGNFVRALNSVL--PEDIVAKDAVEAPGDFHAQFWAKKKTYRYTIFNDTVP 122

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
               +  +  +P  L+ +NMR AA  LVG+HDF+ FR+    A S IRT+   +V   G 
Sbjct: 123 SVFYRRYSLFVPCKLNVDNMRKAASFLVGQHDFSAFRAAGSTARSSIRTMYRAEVEQEGE 182

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
           LI + + A  FL+  +R   G+L  +G GK    +++  + + DR   GP  PP+GL   
Sbjct: 183 LIHVYLEANGFLYNMVRIITGTLLYIGQGKLRVEEMKDIIASGDRTLAGPTVPPQGLCLM 242

Query: 243 SVEY 246
            VEY
Sbjct: 243 RVEY 246


>gi|251792608|ref|YP_003007334.1| tRNA pseudouridine synthase A [Aggregatibacter aphrophilus NJ8700]
 gi|247534001|gb|ACS97247.1| tRNA pseudouridine synthase A [Aggregatibacter aphrophilus NJ8700]
          Length = 261

 Score =  159 bits (402), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 93/252 (36%), Positives = 137/252 (54%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EY+G  YFGWQ+Q+  +S+Q  +E+AI  V  E + +  AGRTDSGVHA  QV
Sbjct: 1   MKIALGVEYDGKQYFGWQKQEKVASVQAELERAISTVANEEISIFCAGRTDSGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA L   D +++    +VD  FHARFSA  R Y Y       
Sbjct: 61  IHFETTANRPEKAWSFGVNANL--PDDVAVRWAKVVDDDFHARFSATARRYRY------- 111

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            L   K R+ ++P+        LD + M  A Q L+G +DF++FR+  CQ+++P R + H
Sbjct: 112 ILYCNKLRSAILPQGVTHCHLELDHQLMHQAGQALLGENDFSSFRAAQCQSNTPWRNVHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V+  G  I + + A +F+H  +R+ VGSL  VG G  +   L   L  +DR    P A
Sbjct: 172 LNVSRQGQYIIVDIQANAFVHHMVRNIVGSLIEVGCGNQSVEWLAWLLAQKDRTLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
            PEGLY  +V Y
Sbjct: 232 KPEGLYLVNVFY 243


>gi|217972794|ref|YP_002357545.1| tRNA pseudouridine synthase A [Shewanella baltica OS223]
 gi|254764864|sp|B8EEB7|TRUA_SHEB2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|217497929|gb|ACK46122.1| tRNA pseudouridine synthase A [Shewanella baltica OS223]
          Length = 261

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 129/245 (52%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+GYFGWQRQ    S+Q  +E+A+ +V  E + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALGIEYDGNGYFGWQRQAEVDSVQAQLERALSIVANEPIGVFCAGRTDAGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA   + D I++  +  VD  FHARFSA  R Y Y I     
Sbjct: 61  VHFETHAIRNEGAWTLGVNA--NLPDNIAVRWVKEVDDSFHARFSATARRYRYVIYNHSF 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              + +         +D + M  AAQ L+G  DFT+FR++ CQ+ +P R +   +V   G
Sbjct: 119 RPGILRHGVSHYHGDIDADRMHQAAQALLGEQDFTSFRAVQCQSKTPFRNVHCVNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             + + + A +FLH  +R+ VGSL  +G G    T +   L  +DR +    A P GLY 
Sbjct: 179 MYVIVDIAANAFLHHMVRNIVGSLLEIGLGNQPLTWMGDLLALKDRNQAAATAKPHGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVTY 243


>gi|240015157|ref|ZP_04722070.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae DGI18]
 gi|240122134|ref|ZP_04735096.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae PID24-1]
          Length = 265

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHAAAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDTTAARPQQAWVRGVNAHLP--EGIAVLHARQVAPGFHARFDAYGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD E M  AA  LVG  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLKLDIEPMCRAASLLVGEQDFSSFRAAGCQAKSPVKTIYRADLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            LI + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLIRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|50083718|ref|YP_045228.1| tRNA pseudouridine synthase A [Acinetobacter sp. ADP1]
 gi|51316594|sp|Q6FEV2|TRUA_ACIAD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|49529694|emb|CAG67406.1| tRNA-pseudouridine synthase I [Acinetobacter sp. ADP1]
          Length = 271

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 92/252 (36%), Positives = 134/252 (53%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE+ G  Y GWQ Q+ G  SIQ +IEK +  +  E +++HGAGRTD+GVHA  
Sbjct: 2   MQRYAVGIEFCGIRYRGWQTQQAGVPSIQETIEKVLSKIADEPIILHGAGRTDAGVHATN 61

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       + A  ++   ISI  +  ++  FHARF A  R Y Y
Sbjct: 62  MVAHFDTNAIRPQRGWL-------MGANSQLPKDISIQWIKEMNTDFHARFKATARRYRY 114

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +   + ++LD + M +AA+   G H+F TFR+  CQ+S P+R + H
Sbjct: 115 VVYNTLNRPALLHKQVTHVYQTLDVDKMMLAARKFEGTHNFETFRAASCQSSQPVRHLSH 174

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G +    ++    AQDRK  G  A
Sbjct: 175 CRLTRHGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGCYEIEHIDTMFAAQDRKAAGVTA 234

Query: 235 PPEGLYFDSVEY 246
           P +GLYF    Y
Sbjct: 235 PADGLYFIQAYY 246


>gi|260914049|ref|ZP_05920522.1| tRNA pseudouridine synthase A [Pasteurella dagmatis ATCC 43325]
 gi|260631682|gb|EEX49860.1| tRNA pseudouridine synthase A [Pasteurella dagmatis ATCC 43325]
          Length = 264

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 98/252 (38%), Positives = 134/252 (53%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + I+YNG  YFGWQRQ+  +S+Q  +EKAI  V  E   +  AGRTDSGVHA  QV
Sbjct: 1   MKVALGIQYNGKNYFGWQRQERVASVQEELEKAISFVANEHCQIFCAGRTDSGVHATGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+             +NA L   D IS+    IVD+ FHARFSA  R Y Y       
Sbjct: 61  IHFETNANRPEKAWSFGVNANL--PDDISVSWAKIVDEDFHARFSANARRYRYI------ 112

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            L   K R+ ++PK        LD + M  A Q L+G +DF++FR+  CQ+ +P R + H
Sbjct: 113 -LYCNKLRSAILPKGITHCHLELDHQLMHQAGQVLLGENDFSSFRASQCQSHTPFRNVHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  I + + A +F+H  +R+ VGSL  +G G      +   L  +DR    P A
Sbjct: 172 LNVIRRGQYIIVDIQANAFVHHMVRNIVGSLIEIGAGHQPVEWMSWLLAQKDRTLAAPTA 231

Query: 235 PPEGLYFDSVEY 246
            PEGLY  +V Y
Sbjct: 232 KPEGLYLVNVIY 243


>gi|330962608|gb|EGH62868.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 274

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 133/251 (52%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 8   RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   IS+    ++   FHARF AI R Y Y I
Sbjct: 68  VHFDTQAERSLKAWV-------MGANINLPHDISVSWARVMPATFHARFKAIARRYRYVI 120

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA HLVG HDF+ FR+  CQA SP++ + H 
Sbjct: 121 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAAHLVGTHDFSAFRAGQCQAKSPVKQLHHL 179

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A 
Sbjct: 180 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWAREVLESKVRRTGGVTAH 239

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 240 PYGLYLVQVEY 250


>gi|110834324|ref|YP_693183.1| tRNA pseudouridine synthase A [Alcanivorax borkumensis SK2]
 gi|123149458|sp|Q0VPI7|TRUA_ALCBS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|110647435|emb|CAL16911.1| Pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 267

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 91/252 (36%), Positives = 132/252 (52%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  + IEY+G+ + GWQ Q++G  ++Q  +E A+  V    V V  AGRTD+GVH   
Sbjct: 1   MTRIALGIEYDGTDFRGWQMQQSGVRTVQECLEAALSKVANHSVTVVCAGRTDAGVHGTG 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
           QV HFD      ++ W+       +     +   ++I     V   FHARFSA+ R Y Y
Sbjct: 61  QVVHFDSDAPREMKSWI-------MGGNTNLPRDVTIRWAVPVSDDFHARFSAVSRRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            I     P AL + +     + LD   MR AA +LVG HDFT +RS+HCQA SP++T+  
Sbjct: 114 VIYNHARPPALYRSQVTWNHRPLDVAAMREAASYLVGHHDFTAYRSVHCQAKSPLKTLHS 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            ++   G ++ +   A +FL   +R+  G L  VG GK      +  L+ +DR+     A
Sbjct: 174 LELYEQGKVLVLEAHANAFLMHMVRNIAGVLMKVGAGKKPPVWAKDVLECRDRRLGAATA 233

Query: 235 PPEGLYFDSVEY 246
           PP GLY   +EY
Sbjct: 234 PPFGLYLVEIEY 245


>gi|184156753|ref|YP_001845092.1| tRNA pseudouridine synthase A [Acinetobacter baumannii ACICU]
 gi|332873165|ref|ZP_08441122.1| tRNA pseudouridine synthase A [Acinetobacter baumannii 6014059]
 gi|238691030|sp|B2I367|TRUA_ACIBC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|183208347|gb|ACC55745.1| Pseudouridylate synthase [Acinetobacter baumannii ACICU]
 gi|322506645|gb|ADX02099.1| truA [Acinetobacter baumannii 1656-2]
 gi|323516520|gb|ADX90901.1| tRNA pseudouridine synthase A [Acinetobacter baumannii TCDC-AB0715]
 gi|332738677|gb|EGJ69547.1| tRNA pseudouridine synthase A [Acinetobacter baumannii 6014059]
          Length = 265

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 134/253 (52%), Gaps = 13/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE++G  Y GWQ Q+ G +S+Q +IE  +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRYAVGIEFSGIQYRGWQTQQPGVASVQETIELVLSKIADEPITLHGAGRTDAGVHATN 60

Query: 60  QVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       + A  ++   ISI  +  +D++FHARF A  R Y Y
Sbjct: 61  MVAHFDTNAIRPERGWI-------MGANSQLPKDISIQWIKQMDEEFHARFKATARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +   I + LD + M  AA    G H+F TFR+  CQ++ P+R + H
Sbjct: 114 VVYNAPHRPALLHKQVTHIYQKLDVQKMIKAASKFEGTHNFETFRAAACQSNQPVRHVKH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G +    ++    A+DRK  G  A
Sbjct: 174 CRLFEHGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDAMFAAEDRKAAGITA 233

Query: 235 PPEGLYFDSVEYS 247
           PP+GLYF    Y 
Sbjct: 234 PPDGLYFIQCYYP 246


>gi|154498331|ref|ZP_02036709.1| hypothetical protein BACCAP_02320 [Bacteroides capillosus ATCC
           29799]
 gi|150272642|gb|EDM99820.1| hypothetical protein BACCAP_02320 [Bacteroides capillosus ATCC
           29799]
          Length = 249

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 86/237 (36%), Positives = 128/237 (54%), Gaps = 2/237 (0%)

Query: 10  YNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVRE 69
           Y G+ Y GWQ QKN  +++ ++EKAI  V G  V   GAGRTD+GVHA   +A+F     
Sbjct: 10  YVGTAYHGWQIQKNAVTVEETLEKAIASVVGHPVKCTGAGRTDAGVHAENYIANFRTTST 69

Query: 70  WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGR 129
                L  A+N   ++ + I ++  + V   F+A  S I++ Y YRI   +   A    R
Sbjct: 70  IPCDRLPLAVNT--RLPEDIVVVKATEVHDGFNAIGSCIKKEYTYRIYNSRIRNAFFVNR 127

Query: 130 AWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVV 189
           AW  PK LD + M+ AA   VG HDF   +S+  +  S +RT+ +F++   G++IE RV 
Sbjct: 128 AWFYPKHLDEKVMQAAADRFVGTHDFAAVQSVGTEVQSTVRTVHYFNMTRSGDMIECRVC 187

Query: 190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           A  FL+  +R+ VG+     +GK+    +   L+ + R   GP APP GLY   + Y
Sbjct: 188 ANGFLYNMVRAMVGTCVYAAEGKFPPEAVSDILEGRCRTAAGPTAPPGGLYMTKLWY 244


>gi|148653728|ref|YP_001280821.1| tRNA pseudouridine synthase A [Psychrobacter sp. PRwf-1]
 gi|148572812|gb|ABQ94871.1| tRNA pseudouridine synthase A [Psychrobacter sp. PRwf-1]
          Length = 302

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 89/249 (35%), Positives = 132/249 (53%), Gaps = 12/249 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + +E+NG+ Y GWQRQ+    +Q  +E+ +  +  E + V  AGRTD+GVH    +AH
Sbjct: 39  YALGVEFNGANYRGWQRQQEVLCVQQVLEETLSKIANEPIEVVAAGRTDAGVHGGNMLAH 98

Query: 64  FDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           F       V  W+     +  N+ L   D I+I  +  +   FHARF AI R Y Y  + 
Sbjct: 99  FTTSAKRGVYNWL-----RGANSLLP--DDIAIRWIQPMPDTFHARFGAIARRYRYITLN 151

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +    A+       I + LD   M+ AA+H+VG HDF++FR+  CQ+  P+R I H  + 
Sbjct: 152 QPQRPAVLNHLVTHIHEPLDLALMQQAAEHIVGTHDFSSFRAAACQSKQPVRNIHHAKLF 211

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I   + A  FLH  +R+ +G+L  +G G+    D  + LQA+DR    P APP+G
Sbjct: 212 KHGEFIVFDIQADGFLHHMVRNLMGTLFAIGKGELQPEDYLRILQAKDRTIAPPTAPPDG 271

Query: 239 LYFDSVEYS 247
           LYF +  Y 
Sbjct: 272 LYFINAYYP 280


>gi|229523210|ref|ZP_04412617.1| tRNA pseudouridine synthase A [Vibrio cholerae TM 11079-80]
 gi|229339573|gb|EEO04588.1| tRNA pseudouridine synthase A [Vibrio cholerae TM 11079-80]
          Length = 264

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 132/246 (53%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + IEY+G+ Y+GWQRQ+   S+Q ++EK++  +    V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGIEYDGTHYYGWQRQREVKSVQEALEKSLSKIANHPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR-Q 120
            HFD   E   V      NA L     I++     V  +FHARFSA  R Y Y I     
Sbjct: 61  VHFDTTAERQMVAWTMGANANL--PKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHVY 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G +      LD E M+ A Q+L+G +DFT+FR++HCQ+ SP R + H +V   
Sbjct: 119 RPGILNSGVS-HYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRSPWRNVMHLNVTRH 177

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + I + A +F+H  +R+  GSL  VG G+     ++  L  +DR      A   GLY
Sbjct: 178 GRYVVIDIKANAFVHHMVRNITGSLIAVGCGEQKPEWIQWLLAQKDRTLAAATAKAGGLY 237

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 238 LVSVDY 243


>gi|255526613|ref|ZP_05393520.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
 gi|296187301|ref|ZP_06855697.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
 gi|255509721|gb|EET86054.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
 gi|296048172|gb|EFG87610.1| tRNA pseudouridine synthase A [Clostridium carboxidivorans P7]
          Length = 247

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 83/241 (34%), Positives = 134/241 (55%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           ++IEY+G+ Y GWQRQ N  SIQ  +E+AI   T     V G+ RTD+GVHA   V +F 
Sbjct: 9   LVIEYDGTNYCGWQRQDNAESIQQKVEEAIERATKVFSKVTGSSRTDAGVHAEGFVCNFF 68

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                 P    +ALN +L   + I I+    VDK+FH+RF++I + Y+Y ++T     A+
Sbjct: 69  TESSIPPENFKEALNVFL--PEDIVIIESKEVDKEFHSRFNSIGKKYVYTVLTGSHRPAI 126

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +   +   K+L+   M+ AA++ +G HDF+ F+       + IRTI   +++  GN I+
Sbjct: 127 RRNYVYYFNKNLNIGQMKEAAKYFLGTHDFSAFKKSGSSVKTSIRTIKELNIDIDGNYIK 186

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
             ++   FL+  +R  VG+L  VG  ++   D++K + +++R   G  AP  GL  + V 
Sbjct: 187 FSIIGDGFLYNMVRIIVGTLLDVGTNRFNPEDIDKIISSKNRSNAGKSAPACGLTLEKVF 246

Query: 246 Y 246
           Y
Sbjct: 247 Y 247


>gi|289623904|ref|ZP_06456858.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289649364|ref|ZP_06480707.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|298486236|ref|ZP_07004299.1| tRNA pseudouridine synthase A [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298159243|gb|EFI00301.1| tRNA pseudouridine synthase A [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|320325326|gb|EFW81393.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320327689|gb|EFW83697.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330869252|gb|EGH03961.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. aesculi
           str. 0893_23]
 gi|330877919|gb|EGH12068.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330891458|gb|EGH24119.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. mori str.
           301020]
 gi|330985608|gb|EGH83711.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 284

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 134/251 (53%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTQAERTMKAWV-------MGANINLPHDVSVTWARVMPATFHARFKAIARRYRYVI 130

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M +AA++LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 131 YNDQIRPAHLNQEITW-NHRPLDVERMALAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A 
Sbjct: 190 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWARDVLESRVRRTGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PYGLYLVQVEY 260


>gi|170767244|ref|ZP_02901697.1| tRNA pseudouridine synthase A [Escherichia albertii TW07627]
 gi|170123578|gb|EDS92509.1| tRNA pseudouridine synthase A [Escherichia albertii TW07627]
          Length = 270

 Score =  159 bits (401), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  ALRKDAAWTLGVNANL--PGDIAVRWVKAVPDDFHARFSATARRYRYIIYNHRLRPAVLS 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHFY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHHQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 252


>gi|291562779|emb|CBL41595.1| pseudouridylate synthase I [butyrate-producing bacterium SS3/4]
          Length = 255

 Score =  159 bits (401), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 133/245 (54%), Gaps = 5/245 (2%)

Query: 6   MIIEYNGSGYFGWQRQKN-GSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF 64
           + +EY+GS Y GWQ+Q N  ++IQG +E  +F + GE + VHG+GRTD+GVHA  QVA+F
Sbjct: 7   ITLEYDGSRYDGWQKQGNTDNTIQGKLENVLFRMAGEEIEVHGSGRTDAGVHARGQVANF 66

Query: 65  DLVREWVP--VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP 122
            +  E  P      + LN YL   D I +L+  IV ++FH+R SA  ++Y Y + T    
Sbjct: 67  HINAEICPDGEAAREYLNRYL--PDDIRVLSAKIVPERFHSRLSATSKTYGYYVETGDKK 124

Query: 123 LALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGN 182
              E+   +   K LD + MR AA+ L+G HDF +F +      S +R ID   +   G 
Sbjct: 125 NVFERKYVYGCGKKLDVKAMRQAAEFLIGEHDFKSFCANRRMKKSTVRRIDEIRIVEHGT 184

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            +E       FL+  +R   G+L  VG G      +++ + A++R   G  APPEGL+  
Sbjct: 185 KLEFLYTGNGFLYNMVRILTGTLLEVGSGTRRPEKMKEIIAAKNRDMAGRTAPPEGLFLL 244

Query: 243 SVEYS 247
            V Y 
Sbjct: 245 HVGYE 249


>gi|218781331|ref|YP_002432649.1| tRNA pseudouridine synthase A [Desulfatibacillum alkenivorans
           AK-01]
 gi|218762715|gb|ACL05181.1| tRNA pseudouridine synthase A [Desulfatibacillum alkenivorans
           AK-01]
          Length = 245

 Score =  159 bits (401), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 92/241 (38%), Positives = 131/241 (54%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +I+EY+G+ Y GWQRQ +  +IQ  +E A+  +T +  VV+GAGRTDSGVHAL  VA+F 
Sbjct: 7   LILEYDGTHYHGWQRQPHDLTIQEVLEGALEKITRQKCVVYGAGRTDSGVHALNYVANFR 66

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
                   +  KALN+ L     I     ++    FHAR SA+ + Y Y I     P A+
Sbjct: 67  CNTHLDAGVFVKALNSTL--PKDIVCKESTLAPDGFHARKSAVSKIYEYHITNGPTPPAV 124

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  AW + + LD E M  AA+  +G HDF+ F       ++ +R I    + S+ N I 
Sbjct: 125 CRQYAWHVRRRLDKEAMTRAAKLFLGSHDFSAFEGAGSPKATSVRNIMQSHIQSWENHII 184

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
            RV A  FL   +R+ VG+L  +G GK     +   L + DR + GP APPEGL+   V+
Sbjct: 185 YRVEANGFLRYMVRNIVGTLVYIGMGKIPPEAVMDILASGDRGQAGPTAPPEGLFMMCVK 244

Query: 246 Y 246
           Y
Sbjct: 245 Y 245


>gi|270157075|ref|ZP_06185732.1| tRNA pseudouridine synthase A [Legionella longbeachae D-4968]
 gi|289164512|ref|YP_003454650.1| tRNA-pseudouridine synthase I [Legionella longbeachae NSW150]
 gi|269989100|gb|EEZ95354.1| tRNA pseudouridine synthase A [Legionella longbeachae D-4968]
 gi|288857685|emb|CBJ11528.1| tRNA-pseudouridine synthase I [Legionella longbeachae NSW150]
          Length = 262

 Score =  159 bits (401), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 93/250 (37%), Positives = 136/250 (54%), Gaps = 12/250 (4%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  +++EY+GS Y GWQ Q    ++Q ++E A+  V    + V  AGRTD+GVHA  QV
Sbjct: 1   MRIALVLEYDGSKYHGWQAQTGLHTVQQAVENALSKVADLPISVVCAGRTDTGVHATNQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      +R W+       +N++L     I +     + ++FHAR+SA  R Y Y I
Sbjct: 61  IHFDSEKQRSIRAWI-----HGVNSFL--PKDICVKWGKELSEEFHARYSATARRYRYVI 113

Query: 117 ITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFD 176
                  AL +       + LD   M  AAQ L+G +DFT+FRS+ CQ+++P+R +    
Sbjct: 114 YNSAIRPALLRSNVTWQYRQLDHRLMHQAAQVLLGENDFTSFRSVECQSNTPMRNVYKLQ 173

Query: 177 VNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPP 236
           VN  G+L+ I + A +FLH  +R+  G L  VG GK     +E+ LQA+DR+     AP 
Sbjct: 174 VNRMGDLVIIDITANAFLHHMVRNIAGVLIAVGSGKRPVFWVEEVLQAKDRRLGAETAPA 233

Query: 237 EGLYFDSVEY 246
            GLY   V Y
Sbjct: 234 YGLYLVQVNY 243


>gi|319787538|ref|YP_004147013.1| tRNA pseudouridine synthase A [Pseudoxanthomonas suwonensis 11-1]
 gi|317466050|gb|ADV27782.1| tRNA pseudouridine synthase A [Pseudoxanthomonas suwonensis 11-1]
          Length = 257

 Score =  158 bits (400), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 91/242 (37%), Positives = 128/242 (52%), Gaps = 4/242 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQR--QKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           +RY + +EY+G G+ GWQ       S++Q ++E+A+  V  + + V  AGRTD+GVHA  
Sbjct: 1   MRYALGVEYDGGGFQGWQGLGPSGPSTVQATLERALSSVADQAITVSCAGRTDAGVHAEC 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QV HFD   E  P      L    ++  T+ +     VD  FHARFSA  R Y Y ++ R
Sbjct: 61  QVVHFDSTAERDPRAW--TLGVTGRLPPTVCVRWCMPVDDAFHARFSARARRYRYTLVNR 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
               AL +       + LD + M  AAQ L+G +DF+ FR++HCQA    R +    V  
Sbjct: 119 PVRPALYRSTMAWERRPLDADAMHRAAQALLGENDFSAFRTVHCQAPHARRNLQDIQVRR 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G  + I V A +FLH  +R+ VGSL  VG G      + + L  +DR   GP A P+GL
Sbjct: 179 SGETVSIEVQANAFLHHMVRNIVGSLLEVGAGARDEGWIARLLAGRDRTLAGPTAAPQGL 238

Query: 240 YF 241
            F
Sbjct: 239 VF 240


>gi|293604664|ref|ZP_06687064.1| tRNA pseudouridine synthase A [Achromobacter piechaudii ATCC 43553]
 gi|292816833|gb|EFF75914.1| tRNA pseudouridine synthase A [Achromobacter piechaudii ATCC 43553]
          Length = 270

 Score =  158 bits (400), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 92/253 (36%), Positives = 138/253 (54%), Gaps = 14/253 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGEIVVVHGAGRTDSGVHAL 58
           M R  + + Y+GS + GWQ Q +  ++Q ++E A+  F    + V    AGRTD+GVH  
Sbjct: 2   MSRVALGLAYDGSAWQGWQTQPHRQTVQDTLESALARFCGVQDPVPTICAGRTDTGVHGA 61

Query: 59  RQVAHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYL 113
            QV H D      +  WV     + +NA+L  S  +S+     V  +FHARFSA  R+Y+
Sbjct: 62  MQVVHLDTSLDRRMESWV-----RGVNAFLPPS--VSVQWAQEVSDEFHARFSARARTYV 114

Query: 114 YRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTID 173
           Y +   +   AL  GRA    ++LD + MR AAQ LVG HDF++FRS  CQA  P+R + 
Sbjct: 115 YLLWRGRVRPALWAGRAGWCFQTLDVDAMRAAAQALVGEHDFSSFRSSQCQAKHPVRHMH 174

Query: 174 HFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPL 233
             D+   G  +   + A +FLH  +R+ +G+L  VG G+ +   + + L  +DR    P 
Sbjct: 175 RLDIAERGPFLVFTLKANAFLHHMVRNIMGALLQVGQGRESVDWMAQLLSLRDRTRGAPT 234

Query: 234 APPEGLYFDSVEY 246
             P+GLY  S++Y
Sbjct: 235 FAPDGLYLSSIDY 247


>gi|71737567|ref|YP_273899.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71558120|gb|AAZ37331.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 274

 Score =  158 bits (400), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 134/251 (53%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 8   RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 68  VHFDTQAERTMKAWV-------MGANINLPHDVSVTWARVMPATFHARFKAIARRYRYVI 120

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M +AA++LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 121 YNDQIRPAHLNQEITW-NHRPLDVERMALAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHL 179

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A 
Sbjct: 180 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWARDVLESRVRRTGGVTAH 239

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 240 PYGLYLVQVEY 250


>gi|262369979|ref|ZP_06063306.1| tRNA-pseudouridine synthase I [Acinetobacter johnsonii SH046]
 gi|262315018|gb|EEY96058.1| tRNA-pseudouridine synthase I [Acinetobacter johnsonii SH046]
          Length = 265

 Score =  158 bits (400), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 90/252 (35%), Positives = 133/252 (52%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R+ + IE+ G+ Y GWQ Q+ G  S+Q +IEK +  +  E + +HGAGRTD+GVHA  
Sbjct: 1   MQRFAIGIEFCGTHYRGWQTQQTGVISVQETIEKVLSKIANEPISLHGAGRTDAGVHATN 60

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       + +  ++   ISI  +  +D+ FHARF A  R Y Y
Sbjct: 61  MVAHFDSSALRSERGWL-------MGSNSQLPKDISIQWIKAMDQDFHARFKAQARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +      +LD   M  AAQ   G H+F +FR+  CQ++ P+R + H
Sbjct: 114 VVYNHPQRPALMHKQVTHAYYALDVAKMMQAAQKFEGTHNFESFRAAACQSNQPVRHVSH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G +    +E    A+DRK  G  A
Sbjct: 174 CRLIQHGPYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEVEHIEAIFAAEDRKAAGITA 233

Query: 235 PPEGLYFDSVEY 246
           PP+GLYF   +Y
Sbjct: 234 PPDGLYFIHADY 245


>gi|320101703|ref|YP_004177294.1| tRNA pseudouridine synthase A [Isosphaera pallida ATCC 43644]
 gi|319748985|gb|ADV60745.1| tRNA pseudouridine synthase A [Isosphaera pallida ATCC 43644]
          Length = 275

 Score =  158 bits (400), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 94/249 (37%), Positives = 132/249 (53%), Gaps = 7/249 (2%)

Query: 1   MIRYC-MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M+R   +I+ Y+G+ + GWQRQ    ++Q  +E A+  +TGE V V  +GRTD+GVHAL 
Sbjct: 1   MLRTLKLILAYDGTEFSGWQRQPGHRTVQEVVESALRPLTGEPVAVTASGRTDAGVHALG 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVAHF  +    P +  KALNA L     + ++      + FHA   A  +S  YR +  
Sbjct: 61  QVAHFHTIARHPPEVFLKALNATLPPD--VRVVWAEEAPQSFHATLDA--QSKRYRYVID 116

Query: 120 QAPLA--LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDV 177
             P A    +  AW + + LD   M  A Q L GRHDF +F +      S +RTI    V
Sbjct: 117 NGPFADPFLRRTAWHLFRPLDAPRMNRAVQALRGRHDFRSFETNWPNRMSSVRTILDVQV 176

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
               + +E+ V A  FL+  +RS  G+  LVG G    T + + L AQDR+  GP APP+
Sbjct: 177 RRIDHRVELEVEADGFLYNMVRSIAGTAVLVGLGDRPETFVAEVLHAQDRRLAGPTAPPQ 236

Query: 238 GLYFDSVEY 246
           GL+   V Y
Sbjct: 237 GLFLLQVRY 245


>gi|59802129|ref|YP_208841.1| tRNA pseudouridine synthase A [Neisseria gonorrhoeae FA 1090]
 gi|62901142|sp|Q5F5V8|TRUA_NEIG1 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|59719024|gb|AAW90429.1| putative tRNA pseudouridine synthase [Neisseria gonorrhoeae FA
           1090]
          Length = 265

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 88/245 (35%), Positives = 132/245 (53%), Gaps = 3/245 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R+ + + Y+GS ++GWQ+Q  G  ++Q ++E A+  + GE V    AGRTD+GVHA  QV
Sbjct: 8   RWAITLSYDGSRFYGWQKQAGGVPTVQAALETALARIAGESVATTVAGRTDTGVHATAQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   + I++L+   V   FHARF A  R Y Y + +   
Sbjct: 68  VHFDTAAVRPAQAWIRGVNAHLP--EGIAVLHARQVAPGFHARFDASGRHYRYLLESAPV 125

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
              L K RA      LD   MR AA  LVG  DF++FR+  CQA SP++TI   D+    
Sbjct: 126 RSPLLKNRAGWTHLELDIGPMRRAAALLVGEQDFSSFRAAGCQAKSPVKTIYRADLTQSA 185

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
            L+ + +   +FLH  +R+ +G+L  VG G+ +       +Q + R +  P   P+GLY 
Sbjct: 186 GLVRLDLHGNAFLHHMVRNIMGALVYVGSGRLSVEGFAALIQERSRLKAPPTFMPDGLYL 245

Query: 242 DSVEY 246
             V+Y
Sbjct: 246 TGVDY 250


>gi|70729445|ref|YP_259183.1| tRNA pseudouridine synthase A [Pseudomonas fluorescens Pf-5]
 gi|68343744|gb|AAY91350.1| tRNA pseudouridine synthase A [Pseudomonas fluorescens Pf-5]
          Length = 274

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 100/251 (39%), Positives = 133/251 (52%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  S+Q ++EKA+  V    VVV  AGRTD+GVHA  QV
Sbjct: 8   RIALGVEYKGSRYRGWQRQASGVPSVQETLEKALSRVADSPVVVSCAGRTDAGVHACGQV 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   IS+     +   FHARF AI R Y Y I
Sbjct: 68  VHFDTQAVRSMKAWV-------MGANINLPHDISVSWAKEMPAHFHARFKAIARRYRYVI 120

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA  LVG HDF+ FR+  CQA SPI+ I H 
Sbjct: 121 YNDQIRPAHLNEEITW-NHRPLDIERMAQAAAFLVGTHDFSAFRAGQCQAKSPIKEIHHL 179

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I + + A +FLH  +R+  G L  +G G+       + L+++ R+  G  A 
Sbjct: 180 RVTRHGKMIVLDIRASAFLHHMVRNIAGVLMTIGAGERPVEWAREVLESRIRRTGGVTAH 239

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 240 PFGLYLVQVEY 250


>gi|257487527|ref|ZP_05641568.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tabaci ATCC
           11528]
 gi|331012647|gb|EGH92703.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tabaci ATCC
           11528]
          Length = 284

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 96/251 (38%), Positives = 133/251 (52%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD   E     WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTQAERTTKAWV-------MGANINLPHDVSVTWARVMPATFHARFKAIARRYRYVI 130

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M +AA++LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 131 YNDQIRPAHLNQEITW-NHRPLDVERMALAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A 
Sbjct: 190 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWARDVLESRVRRTGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PYGLYLVQVEY 260


>gi|190150230|ref|YP_001968755.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|307263568|ref|ZP_07545183.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|238692338|sp|B3GXP8|TRUA_ACTP7 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189915361|gb|ACE61613.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|306871211|gb|EFN02940.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 262

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 96/257 (37%), Positives = 136/257 (52%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      ++ W     C   NA L   D I++     V + FHARFSA  R Y Y I
Sbjct: 61  VHFETQAIRPLQSW-----CFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYII 113

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                     K R+ ++PK        LD + M  A Q L+G +DF++FR+  CQ+ +P 
Sbjct: 114 FN-------NKLRSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPW 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R + H +V+  GN I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR  
Sbjct: 167 RNVHHLNVSRLGNYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTL 226

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A  EGLY   V Y
Sbjct: 227 AAPTAKAEGLYLVDVHY 243


>gi|303251239|ref|ZP_07337417.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307252529|ref|ZP_07534425.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307261387|ref|ZP_07543062.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|302649781|gb|EFL79959.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306860121|gb|EFM92138.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306869118|gb|EFN00920.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
          Length = 262

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 96/257 (37%), Positives = 136/257 (52%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      ++ W     C   NA L   D I++     V + FHARFSA  R Y Y I
Sbjct: 61  VHFETQAIRPLQSW-----CFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYII 113

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                     K R+ ++PK        LD + M  A Q L+G +DF++FR+  CQ+ +P 
Sbjct: 114 FN-------NKLRSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPW 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R + H +V+  GN I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR  
Sbjct: 167 RNVHHLNVSRLGNYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTL 226

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A  EGLY   V Y
Sbjct: 227 AAPTAKAEGLYLVDVHY 243


>gi|307245766|ref|ZP_07527852.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307254739|ref|ZP_07536566.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307259179|ref|ZP_07540909.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306853468|gb|EFM85687.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306862265|gb|EFM94232.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306866846|gb|EFM98704.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 262

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 96/257 (37%), Positives = 136/257 (52%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      ++ W     C   NA L   D I++     V + FHARFSA  R Y Y I
Sbjct: 61  VHFETQAIRPLQSW-----CFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYII 113

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                     K R+ ++PK        LD + M  A Q L+G +DF++FR+  CQ+ +P 
Sbjct: 114 FN-------NKLRSAILPKGISHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPW 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R + H +V+  GN I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR  
Sbjct: 167 RNVHHLNVSRLGNYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTL 226

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A  EGLY   V Y
Sbjct: 227 AAPTAKAEGLYLVDVHY 243


>gi|46143880|ref|ZP_00204588.1| COG0101: Pseudouridylate synthase [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
          Length = 262

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 96/257 (37%), Positives = 136/257 (52%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      ++ W     C   NA L   D I++     V + FHARFSA  R Y Y I
Sbjct: 61  VHFETQAIRPLQSW-----CFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYII 113

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                     K R+ ++PK        LD + M  A Q L+G +DF++FR+  CQ+ +P 
Sbjct: 114 FN-------NKLRSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPW 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R + H +V+  GN I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR  
Sbjct: 167 RNVHHLNVSRLGNYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTL 226

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A  EGLY   V Y
Sbjct: 227 AAPTAKAEGLYLVDVHY 243


>gi|226951929|ref|ZP_03822393.1| tRNA-pseudouridine synthase I [Acinetobacter sp. ATCC 27244]
 gi|294649190|ref|ZP_06726629.1| tRNA pseudouridine synthase A [Acinetobacter haemolyticus ATCC
           19194]
 gi|226837469|gb|EEH69852.1| tRNA-pseudouridine synthase I [Acinetobacter sp. ATCC 27244]
 gi|292824908|gb|EFF83672.1| tRNA pseudouridine synthase A [Acinetobacter haemolyticus ATCC
           19194]
          Length = 265

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 134/252 (53%), Gaps = 13/252 (5%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M RY + IE+ G+ Y GWQ Q+ G +S+Q +IEK +  +    +++HGAGRTD+GVHA  
Sbjct: 1   MQRYAIGIEFCGTQYRGWQTQQAGVASVQETIEKVLSTIADHPIILHGAGRTDAGVHATN 60

Query: 60  QVAHFDLV-----REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLY 114
            VAHFD       R W+       +    ++   IS+  +  +D+ FHARF A  R Y Y
Sbjct: 61  MVAHFDTTAIRPDRGWL-------MGTNSQLPKDISLQWIKRMDESFHARFKARARRYRY 113

Query: 115 RIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            +       AL   +   + ++LD + M  AA    G H+F TFR+  CQ++ P+R + H
Sbjct: 114 IVYNAPTRPALLYKQVTHLYQTLDVQKMIAAAAKFEGTHNFETFRAAACQSNQPVRHVKH 173

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
             +   G  + + + A  FLH  +R+ +G L  +G G +    ++    AQDRK  G  A
Sbjct: 174 CRLFEHGRYLVLDIQADGFLHHMVRNIMGCLLEIGQGMYEIDHIDHMFAAQDRKAAGITA 233

Query: 235 PPEGLYFDSVEY 246
           P +GLYF   EY
Sbjct: 234 PADGLYFIQAEY 245


>gi|145641169|ref|ZP_01796749.1| tRNA pseudouridine synthase A [Haemophilus influenzae R3021]
 gi|145274006|gb|EDK13872.1| tRNA pseudouridine synthase A [Haemophilus influenzae 22.4-21]
          Length = 269

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 131/245 (53%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEYNG  Y+GWQRQ+   S+Q  +EKA+  +  E + +  AGRTDSGV    QV
Sbjct: 1   MKIALGIEYNGQNYYGWQRQEKVRSVQEELEKALSCIANEKIEIFCAGRTDSGVSGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+              NA+L   D I++     VD +FHARFSA  R Y Y +   + 
Sbjct: 61  VHFETNVIRPEKAWAFGTNAHL--PDDIAVSWAKQVDDEFHARFSATARRYRYILYCNKL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+  G        LD E M  A Q L+G HDF++FR+  CQ+ +P R + H +V+  G
Sbjct: 119 RSAILAGGITHCHLDLDAEKMHQAGQCLLGEHDFSSFRAAQCQSHTPWRNVHHLNVSRIG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I + + A +F+H  +R+ VGSL  VG G      ++  L+ ++R+   P A P+GLY 
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNKPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 VDVIY 243


>gi|251788988|ref|YP_003003709.1| tRNA pseudouridine synthase A [Dickeya zeae Ech1591]
 gi|247537609|gb|ACT06230.1| tRNA pseudouridine synthase A [Dickeya zeae Ech1591]
          Length = 276

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 135/247 (54%), Gaps = 6/247 (2%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS Y+GWQRQ    S+QG +E A+  V    + V  AGRTD+GVHA  QV
Sbjct: 13  LKIALGIEYDGSRYYGWQRQAEVDSVQGCLEAALSQVANARIDVFCAGRTDAGVHATGQV 72

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ- 120
            HF              +NA L     I++  +  VD+ FHARFSA  R Y Y I  R+ 
Sbjct: 73  VHFTTHAVRKDAAWTMGVNANLPPD--IAVRWVKTVDEAFHARFSATARRYRYVIYNRRF 130

Query: 121 APLALEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
            P  L +G   + +P  LD E M  A Q L+G +DFT+FR++ CQ+ +P R + H  V  
Sbjct: 131 RPAILSQGVTHYYLP--LDAERMHRAGQCLLGENDFTSFRAVQCQSRTPWRNLMHLRVTR 188

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
            G+ + + + A +F+H  +R+ VGSL  +G G      + + L A+DR      A  +GL
Sbjct: 189 LGDYVVVDIKANAFVHHMVRNIVGSLMEIGCGNQPENWMAELLAAKDRTLAAATAKADGL 248

Query: 240 YFDSVEY 246
           Y  +V+Y
Sbjct: 249 YLVAVDY 255


>gi|297538368|ref|YP_003674137.1| tRNA pseudouridine synthase A [Methylotenera sp. 301]
 gi|297257715|gb|ADI29560.1| tRNA pseudouridine synthase A [Methylotenera sp. 301]
          Length = 272

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 89/245 (36%), Positives = 127/245 (51%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + + Y+G+ + GWQ Q NG  +Q ++E AI  +    V VH AGRTD+GVHA  QV
Sbjct: 1   MRISLCLAYDGANFCGWQSQSNGGGVQDALELAISSIAQHQVRVHAAGRTDTGVHARCQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD           + +NA+L   +T+ +     VD+ FHARFSA  RSY Y +     
Sbjct: 61  VHFDTTSIRPLTAWVRGVNAHLP--ETVRVEWAHEVDEDFHARFSAFSRSYQYLLYNAPV 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL   +A      L+ E M  AA +LVG HDF+ FR+  CQA +  R +   +V   G
Sbjct: 119 APALMATKAGWFHLPLNGEAMSEAASYLVGEHDFSGFRASECQAKTATRNMIKSEVKVAG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
                   A +FL  Q+R+ +G+L  +G G +    +++ LQ +DR    P   P GLY 
Sbjct: 179 KYFIFEFSANAFLQHQVRNMIGALVYIGKGAYPPIYMKELLQKRDRTLSPPTFSPNGLYL 238

Query: 242 DSVEY 246
             V Y
Sbjct: 239 TGVGY 243


>gi|78485146|ref|YP_391071.1| tRNA pseudouridine synthase A [Thiomicrospira crunogena XCL-2]
 gi|123741632|sp|Q31HH6|TRUA_THICR RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|78363432|gb|ABB41397.1| tRNA pseudouridine synthase A [Thiomicrospira crunogena XCL-2]
          Length = 262

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 87/239 (36%), Positives = 133/239 (55%), Gaps = 2/239 (0%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY G+ Y GWQ QK+  S+Q  +EKA+  +  E + ++ AGRTD+GVHA+ Q+AHF+  
Sbjct: 8   IEYQGTAYCGWQHQKHCDSVQQQLEKALSYIADEPIGLNCAGRTDTGVHAIGQIAHFETN 67

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK 127
                    + +N   ++ + I +  +  + + FHARFSA+ R Y Y I  R    A+  
Sbjct: 68  ASRPDKAWIQGVNT--QLPNDIRVTWVKPMPEDFHARFSAVARQYRYVIFNRPVHSAILA 125

Query: 128 GRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIR 187
            R     + LD + M  AAQ L+G +DF++FR+  CQAS   R + +  V+  GN + + 
Sbjct: 126 NRVTWENRPLDVKKMHAAAQDLLGENDFSSFRAAGCQASHANRNVQYLQVSRQGNFVFVD 185

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
           + A +FLH  +R+ VG+L  VG        + + L+ QDR + G  AP  GLYF +  Y
Sbjct: 186 IQANAFLHHMVRNIVGTLLEVGRLDKPVEWVSELLKKQDRTQAGMTAPAAGLYFVNALY 244


>gi|312877809|ref|ZP_07737759.1| tRNA pseudouridine synthase A [Caldicellulosiruptor lactoaceticus
           6A]
 gi|311795435|gb|EFR11814.1| tRNA pseudouridine synthase A [Caldicellulosiruptor lactoaceticus
           6A]
          Length = 244

 Score =  158 bits (399), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 89/241 (36%), Positives = 135/241 (56%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q A+F 
Sbjct: 6   LTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQKANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +        ALN+ L     IS+ +   V   F AR+SA +++Y Y I  +++  AL
Sbjct: 66  TNSKIPTDKFPLALNSVL--PGDISVKDAVEVPLDFSARYSAKQKTYKYLIYNKKSRPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR + +  +      I 
Sbjct: 124 LRNYAYYYPYELDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRRVYNAYLTFENECIA 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY   V 
Sbjct: 184 IYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLVIESKDRTKAGKTLPPWGLYLVDVV 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|283786396|ref|YP_003366261.1| tRNA pseudouridine synthase A [Citrobacter rodentium ICC168]
 gi|282949850|emb|CBG89473.1| tRNA pseudouridine synthase A [Citrobacter rodentium ICC168]
          Length = 269

 Score =  158 bits (399), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 131/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           +EY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 15  VEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETS 74

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V + FHARFSA  R Y Y I   R  P  L 
Sbjct: 75  ALRKDAAWTLGVNANL--PGDIAVRWVKAVPEDFHARFSATARRYRYIIYNHRLRPAVLA 132

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+  G  + +
Sbjct: 133 KGVTHYY-EPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVSRHGAYVVV 191

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 192 DIKANAFVHHMVRNIVGSLMEVGAHHQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDY 251


>gi|260584448|ref|ZP_05852195.1| tRNA pseudouridine synthase A [Granulicatella elegans ATCC 700633]
 gi|260157966|gb|EEW93035.1| tRNA pseudouridine synthase A [Granulicatella elegans ATCC 700633]
          Length = 250

 Score =  158 bits (399), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 91/246 (36%), Positives = 133/246 (54%), Gaps = 3/246 (1%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT-GEIVVVHGAGRTDSGVHALRQV 61
           RY +I+ Y+G+ Y G+Q Q+NG+SIQ  + KA+  +T G  + V G+GRTDSGVHA  QV
Sbjct: 4   RYKVILSYDGTNYVGFQVQENGNSIQAELNKALRKMTKGLYIPVCGSGRTDSGVHANGQV 63

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD   +     L +ALN+ L   D IS   +  V  +FHAR+S   + Y+YR+  ++ 
Sbjct: 64  IHFDYPTKIEEENLQRALNSLL--PDDISAKQVMAVSDEFHARYSVTGKRYIYRVNIQKF 121

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
                +      P  ++ +NM  A Q ++G HDFT+F S      S +R +   +V    
Sbjct: 122 VNPFSRLYTLHHPYRVNVDNMNEALQAVIGEHDFTSFCSTKTDKESKVRIVTKAEVVEKD 181

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             +        FL+  IR  VG+   +GDG    +D+   L A DR++ GP APP+GLY 
Sbjct: 182 GELVFTFEGNGFLYNMIRILVGTSLQIGDGLRPVSDMRDILVAMDRQKAGPTAPPQGLYL 241

Query: 242 DSVEYS 247
           D V Y 
Sbjct: 242 DEVFYE 247


>gi|126208378|ref|YP_001053603.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae L20]
 gi|166228675|sp|A3N0R2|TRUA_ACTP2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|126097170|gb|ABN73998.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 262

 Score =  158 bits (399), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 95/257 (36%), Positives = 137/257 (53%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      ++ W     C   NA L   D I++     V + FHARFSA  R Y Y I
Sbjct: 61  VHFETQAIRPLQSW-----CFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYII 113

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                     K R+ ++PK       +LD + M +A Q L+G +DF++FR+  CQ+ +P 
Sbjct: 114 FN-------NKLRSAILPKGVSHYHYALDHQKMHVAGQFLLGENDFSSFRAAKCQSHTPW 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R + H +V+  GN I + + A +F+H  +R+ V SL  VG G+     ++  L  +DR  
Sbjct: 167 RNVHHLNVSRLGNYIVVDIQANAFVHHMVRNIVESLIEVGQGRQPVEWIQWLLAQRDRTL 226

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A  EGLY   V Y
Sbjct: 227 AAPTAKAEGLYLVDVHY 243


>gi|329297440|ref|ZP_08254776.1| tRNA pseudouridine synthase A [Plautia stali symbiont]
          Length = 270

 Score =  158 bits (399), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 94/246 (38%), Positives = 130/246 (52%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
            +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V    V V  AGRTD+GVH   QV
Sbjct: 8   FKLALGIEYDGSRYYGWQRQNEVRSVQEKLEKALAKVANHPVNVFCAGRTDAGVHGTGQV 67

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF+             +N+   + D I++  +  V + FHARFSA  R Y Y I   R 
Sbjct: 68  VHFETTLSRADSAWTLGVNS--NLPDDIAVRWVKAVPETFHARFSATARRYRYVIYNQRL 125

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L KG        LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H  V   
Sbjct: 126 RPAILGKGITHFY-HPLDAEKMHRAAQALLGENDFTSFRAVQCQSRTPWRNVMHLYVTRQ 184

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + + + A +F+H  +R+ VGSL  +G G    T +   L A+DR      A  EGLY
Sbjct: 185 GPYVIVDIKANAFVHYMVRNIVGSLLEIGCGNQPETWMATLLAAKDRTLAAATAKAEGLY 244

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 245 LVAVDY 250


>gi|226949212|ref|YP_002804303.1| tRNA pseudouridine synthase A [Clostridium botulinum A2 str. Kyoto]
 gi|226843950|gb|ACO86616.1| tRNA pseudouridine synthase A [Clostridium botulinum A2 str. Kyoto]
          Length = 246

 Score =  158 bits (399), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 137/247 (55%), Gaps = 3/247 (1%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M    + I+Y+GS Y GWQ+QK N ++IQG IE  + L+T E + +  +GRTD+GVHA  
Sbjct: 1   MTNIKLYIQYDGSKYNGWQKQKENDNTIQGKIENVLSLMTREDINLIASGRTDTGVHANM 60

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
           QVA+F    +     +      YL     I + +   VD++FH+R +  ++ Y Y+I  +
Sbjct: 61  QVANFHTTFQGSTDEILNYCYEYL--PKDIVVYDAFHVDERFHSRLNVKKKKYTYKICNK 118

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNS 179
           +      +  ++ IP++LD   M+ A  +LVGRHDF +F +   +  S +RT+   D+  
Sbjct: 119 KFHDVFSRKYSYHIPETLDINAMKEACTYLVGRHDFASFTAARSKKKSTVRTLYSIDIIK 178

Query: 180 FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL 239
               +++  +   FLH  IR   G+L  VG     S D++  L A+DR++ GP AP +GL
Sbjct: 179 KDGYVDLVYLGSGFLHKMIRILTGTLIEVGLHNLKSVDVKNILTAEDRRKAGPTAPSQGL 238

Query: 240 YFDSVEY 246
           +  SV+Y
Sbjct: 239 FMTSVDY 245


>gi|187933357|ref|YP_001884507.1| tRNA pseudouridine synthase A [Clostridium botulinum B str. Eklund
           17B]
 gi|238691608|sp|B2TIK9|TRUA_CLOBB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|187721510|gb|ACD22731.1| tRNA pseudouridine synthase A [Clostridium botulinum B str. Eklund
           17B]
          Length = 244

 Score =  158 bits (399), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 134/242 (55%), Gaps = 4/242 (1%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           +IIE++G+ + GWQRQ    ++QG +EKAI  +TGE  + +G+ RTD GVHA   VA+F 
Sbjct: 6   LIIEFDGTNFCGWQRQIKDRTVQGCLEKAILKITGEKSLTNGSSRTDGGVHAKAMVANF- 64

Query: 66  LVREWVP-VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLA 124
           +    +P     +ALN   K+ D I+++    VD  FHAR+S+  + Y Y I+ R   L+
Sbjct: 65  ITNSSIPGEKFREALNT--KLPDDIAVIKSEEVDMDFHARYSSKGKMYSYTIVNRYEKLS 122

Query: 125 LEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLI 184
             K     + K L+ E+M+ A +  +G+HDF  F S    A + +RTI  F +    ++I
Sbjct: 123 FGKQYVHHVRKELNVEDMKKACECFIGKHDFKAFMSPGSSAKTTVRTIQEFYIEKNEDVI 182

Query: 185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSV 244
           +I + A  FL+  +R  VG+L  +G GK    D++  +    RK  G   PP GL  + V
Sbjct: 183 KIFISADGFLYNMVRIIVGTLINIGTGKTKLEDVDNIINDGIRKRSGMCVPPNGLVLEKV 242

Query: 245 EY 246
            Y
Sbjct: 243 FY 244


>gi|330446609|ref|ZP_08310261.1| tRNA pseudouridine synthase A [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328490800|dbj|GAA04758.1| tRNA pseudouridine synthase A [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 261

 Score =  157 bits (398), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G+ Y+GWQRQ++  S+Q  +EKA+  V  + + V  AGRTD+GVH   QV
Sbjct: 1   MRIALGVEYDGAKYYGWQRQRDVDSVQERLEKALSKVANQPIEVFCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HFD+  +   V      NA L     I++   + V + FHARF+A  R Y Y I     
Sbjct: 61  VHFDVNIDRKMVAWTMGANANL--PKDIAVRWATEVSEDFHARFTATARRYRYIIFNNAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q+L+G +DFT+FR++HCQ+ SP R + H  V   G
Sbjct: 119 RPAILGTGVSHYHGHLDEKKMHEAGQYLLGENDFTSFRAVHCQSRSPWRNLMHLKVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  VG G+     ++  L+ +DR   G  A  EGLY 
Sbjct: 179 DFVIIDIKANAFVHHMVRNITGSLIKVGKGEEKPEWIKWLLEQKDRTLAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|312793879|ref|YP_004026802.1| tRNA pseudouridine synthase a [Caldicellulosiruptor kristjanssonii
           177R1B]
 gi|312181019|gb|ADQ41189.1| tRNA pseudouridine synthase A [Caldicellulosiruptor kristjanssonii
           177R1B]
          Length = 244

 Score =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 90/241 (37%), Positives = 135/241 (56%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q A+F 
Sbjct: 6   LTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQKANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +        ALN+ L     ISI +   V   F AR+SA +++Y Y I  +++  AL
Sbjct: 66  TNSKIPTDKFPLALNSVL--PGDISIKDAVEVPLDFSARYSAKQKTYKYLIYNKKSRPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR + +  +      I 
Sbjct: 124 LRNYAYHYPYELDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRRVYNAYLTFENECIA 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I + A  FL+   R   G++  VG GK    D+   ++++DR + G   PP GLY   V 
Sbjct: 184 IYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLVIESKDRTKAGKTLPPWGLYLVDVV 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|330952706|gb|EGH52966.1| tRNA pseudouridine synthase A [Pseudomonas syringae Cit 7]
          Length = 274

 Score =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 134/251 (53%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 8   RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 68  VHFDTQAERTMKAWV-------MGANINLPHDVSVTWARVMPATFHARFKAIARRYRYVI 120

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 121 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHL 179

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A 
Sbjct: 180 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWAREVLESRIRRTGGVTAH 239

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 240 PYGLYLVGVEY 250


>gi|238897977|ref|YP_002923657.1| pseudouridylate synthase I [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
 gi|229465735|gb|ACQ67509.1| pseudouridylate synthase I [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
          Length = 277

 Score =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 99/244 (40%), Positives = 139/244 (56%), Gaps = 11/244 (4%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHF--D 65
           IEYNG  Y+GWQRQ++  SIQ  +E A+  +  E + V  AGRTD+GVHA  QV HF   
Sbjct: 21  IEYNGYRYYGWQRQEHVPSIQSCLEHALSKIANESITVCCAGRTDAGVHATAQVVHFLTK 80

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLA 124
            VR+ V  I+   +N YL     I++     V+K FHARFSA  R Y Y I   R  P  
Sbjct: 81  AVRKEVSWIM--GVNTYL--PPDITVRWAKKVEKDFHARFSATARRYRYLIFNDRHRPAL 136

Query: 125 LEKGRA-WLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG-N 182
             +G A + +P  LD + M  AAQ ++G +DF++FR+  CQ+ +P R + H  V+ FG +
Sbjct: 137 FSEGLAHYSMP--LDEKKMERAAQCVLGENDFSSFRAAQCQSKTPWRYVHHLKVSRFGMH 194

Query: 183 LIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFD 242
            I + + A +FLH  +R+ VGSL  VG G+     + + L  +DR +    A   GLY  
Sbjct: 195 YIMVDIKANAFLHHMVRNIVGSLIEVGIGRQNEHWIAQLLALKDRTQAAVTAKASGLYLV 254

Query: 243 SVEY 246
           SV+Y
Sbjct: 255 SVDY 258


>gi|330901134|gb|EGH32553.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 284

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 134/251 (53%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTQAERTLKAWV-------MGANINLPHDVSVTWARVMPATFHARFKAIARRYRYVI 130

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 131 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A 
Sbjct: 190 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWAREVLESRIRRTGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PYGLYLVGVEY 260


>gi|289671992|ref|ZP_06492882.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. syringae
           FF5]
 gi|330975198|gb|EGH75264.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 274

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 134/251 (53%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 8   RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 68  VHFDTQAERTLKAWV-------MGANINLPHDVSVTWARVMPATFHARFKAIARRYRYVI 120

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 121 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHL 179

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A 
Sbjct: 180 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWAREVLESRIRRTGGVTAH 239

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 240 PYGLYLVGVEY 250


>gi|89073216|ref|ZP_01159746.1| tRNA pseudouridine synthase A [Photobacterium sp. SKA34]
 gi|89050926|gb|EAR56390.1| tRNA pseudouridine synthase A [Photobacterium sp. SKA34]
          Length = 261

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 90/245 (36%), Positives = 135/245 (55%), Gaps = 2/245 (0%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+G+ Y+GWQRQ++  S+Q  +EKA+  V  + V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGVEYDGAKYYGWQRQRDVDSVQERLEKALSKVANQPVEVFCAGRTDAGVHGTGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF++  +   V      NA+L     I++   + V + FHARF+A  R Y Y I     
Sbjct: 61  VHFEINIDRKIVAWTMGANAHL--PKDIAVRWATEVSEDFHARFTATARRYRYIIFNNAL 118

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             A+           LD + M  A Q+L+G +DFT+FR++HCQ+ SP R + H +V   G
Sbjct: 119 RPAILGNGVSHYHGHLDEKKMHEAGQYLLGENDFTSFRAMHCQSRSPWRNLIHLNVTRQG 178

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
           + + I + A +F+H  +R+  GSL  VG G+     +E  L  ++R   G  A  EGLY 
Sbjct: 179 DFVIIDIKANAFVHHMVRNITGSLIKVGKGEEKPEWIEWLLAQKNRTLAGATAKAEGLYL 238

Query: 242 DSVEY 246
             V+Y
Sbjct: 239 VDVDY 243


>gi|330943525|gb|EGH45866.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 284

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 134/251 (53%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTQAERTLKAWV-------MGANINLPHDVSVTWARVMPATFHARFKAIARRYRYVI 130

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 131 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A 
Sbjct: 190 RVTHHGKMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPVEWAREVLESRIRRTGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PYGLYLVGVEY 260


>gi|66044907|ref|YP_234748.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. syringae
           B728a]
 gi|63255614|gb|AAY36710.1| tRNA pseudouridine synthase [Pseudomonas syringae pv. syringae
           B728a]
          Length = 284

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 134/251 (53%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTQAERSMKAWV-------MGANINLPHDVSVTWARVMPATFHARFKAIARRYRYVI 130

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 131 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A 
Sbjct: 190 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPIEWAREVLESRIRRTGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PYGLYLVGVEY 260


>gi|330973842|gb|EGH73908.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 274

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/251 (37%), Positives = 134/251 (53%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 8   RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 68  VHFDTQAERSMKAWV-------MGANINLPHDVSVTWARVMPATFHARFKAIARRYRYVI 120

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA++LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 121 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPVKQLHHL 179

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+       + L+++ R+  G  A 
Sbjct: 180 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGTGERPIEWAREVLESRIRRTGGVTAH 239

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 240 PYGLYLVGVEY 250


>gi|332970004|gb|EGK09003.1| tRNA pseudouridine synthase A [Psychrobacter sp. 1501(2011)]
          Length = 314

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 89/249 (35%), Positives = 132/249 (53%), Gaps = 12/249 (4%)

Query: 4   YCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH 63
           Y + IE+NGS Y GWQRQ+    +Q  +E+ +  +  E + V  AGRTD+GVH    +AH
Sbjct: 52  YALGIEFNGSNYRGWQRQQEVLCVQQVLEETLSKIANEPIEVVAAGRTDAGVHGGNMLAH 111

Query: 64  FDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT 118
           F       V  W+     +  N+ L   D I+I  +  +   FHARF AI R Y Y  + 
Sbjct: 112 FKTSANRGVYNWL-----RGANSLLP--DDIAIRWIQPMPDDFHARFGAIARRYRYITLN 164

Query: 119 RQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVN 178
           +    A+       I + LD   M+ AA H+VG+HDF++FR+  CQ++ P+R I H  + 
Sbjct: 165 QPQRPAVLNHLVTHIHEPLDLAKMQQAAAHIVGQHDFSSFRAAACQSNQPVRNIHHAKLF 224

Query: 179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEG 238
             G  I   + A  FLH  +R+ +G+L  +G G+    D  + L+A+DR    P A P+G
Sbjct: 225 QHGQFIVFDIQADGFLHHMVRNLMGTLFAIGKGELQPMDYLRILEAKDRTIAPPTASPDG 284

Query: 239 LYFDSVEYS 247
           LYF +  Y 
Sbjct: 285 LYFINAYYP 293


>gi|302871559|ref|YP_003840195.1| tRNA pseudouridine synthase A [Caldicellulosiruptor obsidiansis
           OB47]
 gi|302574418|gb|ADL42209.1| tRNA pseudouridine synthase A [Caldicellulosiruptor obsidiansis
           OB47]
          Length = 244

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 135/245 (55%), Gaps = 10/245 (4%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q A+F 
Sbjct: 6   LTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQKANFK 65

Query: 66  ----LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
               +  +  P+ L   L   + + D I       V   F AR+SA +++Y Y I  +++
Sbjct: 66  TSSKIPTDKFPLALNSVLPGDISVKDAIE------VSLDFSARYSAKQKTYKYLIYNKKS 119

Query: 122 PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFG 181
             AL +  A+  P  LD + M+ A ++ +G +DF +F S+  ++ + +R I +  +    
Sbjct: 120 RPALLRNYAYYYPYELDVDAMQRACEYFIGEYDFKSFCSVDSESKTTVRRIYNAYLTFEN 179

Query: 182 NLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF 241
             I I + A  FL+   R   G++  VG GK    D+   ++++DR   G   PP GLY 
Sbjct: 180 ECIAIYLTANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTLAGKTLPPWGLYL 239

Query: 242 DSVEY 246
             V Y
Sbjct: 240 VDVAY 244


>gi|157144741|ref|YP_001452060.1| tRNA pseudouridine synthase A [Citrobacter koseri ATCC BAA-895]
 gi|166228694|sp|A8ADR1|TRUA_CITK8 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|157081946|gb|ABV11624.1| hypothetical protein CKO_00468 [Citrobacter koseri ATCC BAA-895]
          Length = 270

 Score =  157 bits (396), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E V V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPVNVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V + FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  ALRKDAAWTLGVNANL--PGDIAVRWVKAVPEDFHARFSATARRYRYIIYNHRLRPAILG 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
            G      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 HGVTHFY-EPLDAERMHRAAQCLIGENDFTSFRAVQCQSRTPWRNVMHINVTRHGAYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR+     A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRRLSAATAKAEGLYLVAVDY 252


>gi|237800363|ref|ZP_04588824.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. oryzae str.
           1_6]
 gi|331023220|gb|EGI03277.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. oryzae str.
           1_6]
          Length = 284

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/251 (38%), Positives = 132/251 (52%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYCGWQRQASGVLTVQETLENALSKVAASPVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDLVRE-----WVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD + E     WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTLAERSLKAWV-------MGANINLPHDVSVTWARVMPANFHARFKAIARRYRYVI 130

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA+ LVG HDF+ FR+  CQA SP++ + H 
Sbjct: 131 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEFLVGTHDFSAFRAGQCQAKSPVKQLHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A 
Sbjct: 190 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWARDVLESRVRRTGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PYGLYLVQVEY 260


>gi|253579808|ref|ZP_04857076.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848807|gb|EES76769.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 246

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 133/246 (54%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           M R  +++ Y+G+ Y GWQ Q NG ++QG +   +  + GE +   GA RTD+GVHA+  
Sbjct: 1   MKRIGLVVAYDGTNYCGWQTQPNGITVQGVLNDTLSELLGEKIETIGASRTDAGVHAMGN 60

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           VA FD         +  ALN   ++ + I I     V+  FH R+    ++Y YRI+ R+
Sbjct: 61  VAVFDTNTRIPGEKISYALNQ--RLPEDIRIQLSEEVEPDFHPRYCDSEKTYEYRILNRK 118

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P+  E+   +     LD + M+ A  +L+G+HDF +F     Q  + IRT+   DV   
Sbjct: 119 FPVPTERLYTYFYHYKLDVDKMKAATSYLIGQHDFASFCGAKAQVKTTIRTVTGIDVWRD 178

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+++ IRV    FL+  +R   G+L  VG+G++    ++  L+A +R+  GP AP +GL 
Sbjct: 179 GDIVTIRVTGTGFLYNMVRIISGTLIEVGNGQYPPERVKTILEACNREMAGPTAPAQGLT 238

Query: 241 FDSVEY 246
              +E+
Sbjct: 239 LMGIEF 244


>gi|303252899|ref|ZP_07339058.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307247890|ref|ZP_07529926.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|302648329|gb|EFL78526.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306855692|gb|EFM87859.1| tRNA pseudouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
          Length = 262

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 95/257 (36%), Positives = 136/257 (52%), Gaps = 26/257 (10%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + IEY+GS YFGWQRQ    S+Q  +E+A+ +V    + V  AGRTDSGVH   QV
Sbjct: 1   MKIALGIEYDGSRYFGWQRQDEVESVQQKLEEALSIVANAPIEVFCAGRTDSGVHGTGQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HF+      ++ W     C   NA L   D I++     V + FHARFSA  R Y Y I
Sbjct: 61  VHFETQAIRPLQSW-----CFGTNANL--PDDIAVKWAVEVSEDFHARFSATARRYRYII 113

Query: 117 ITRQAPLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPI 169
                     K R+ ++PK        LD + M  A Q L+G +DF++FR+  CQ+ +P 
Sbjct: 114 FN-------NKPRSAILPKGVSHYHYELDHQKMHEAGQFLLGENDFSSFRAAKCQSHTPW 166

Query: 170 RTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           R + + +V+  GN I + + A +F+H  +R+ VGSL  VG G+     ++  L  +DR  
Sbjct: 167 RNVHYLNVSRLGNYIVVDIQANAFVHHMVRNIVGSLIEVGQGRQPVEWIQWLLAQRDRTL 226

Query: 230 CGPLAPPEGLYFDSVEY 246
             P A  EGLY   V Y
Sbjct: 227 AAPTAKAEGLYLVDVHY 243


>gi|302060553|ref|ZP_07252094.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tomato K40]
          Length = 284

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/251 (38%), Positives = 133/251 (52%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 18  RIALGVEYKGSRYCGWQRQASGVLTVQETLENALSKVAASPVSLMCAGRTDAGVHACGQV 77

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 78  VHFDTQAERSLKAWV-------MGANINLPHDVSVSWARVMPATFHARFKAIARRYRYVI 130

Query: 117 ITRQA-PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA++LVG HDF+ FR+  CQA SPI+ + H 
Sbjct: 131 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPIKQLHHL 189

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A 
Sbjct: 190 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWARDVLESRVRRTGGVTAH 249

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 250 PYGLYLVQVEY 260


>gi|162533082|ref|YP_001621406.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|213971672|ref|ZP_03399779.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tomato T1]
 gi|301386519|ref|ZP_07234937.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tomato
           Max13]
 gi|302134665|ref|ZP_07260655.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|118201619|gb|ABK79682.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|213923557|gb|EEB57145.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. tomato T1]
 gi|331019139|gb|EGH99195.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 274

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/251 (38%), Positives = 133/251 (52%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 8   RIALGVEYKGSRYCGWQRQASGVLTVQETLENALSKVAASPVSLMCAGRTDAGVHACGQV 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 68  VHFDTQAERSLKAWV-------MGANINLPHDVSVSWARVMPATFHARFKAIARRYRYVI 120

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA++LVG HDF+ FR+  CQA SPI+ + H 
Sbjct: 121 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPIKQLHHL 179

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A 
Sbjct: 180 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWARDVLESRVRRTGGVTAH 239

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 240 PYGLYLVQVEY 250


>gi|226327923|ref|ZP_03803441.1| hypothetical protein PROPEN_01804 [Proteus penneri ATCC 35198]
 gi|225203627|gb|EEG85981.1| hypothetical protein PROPEN_01804 [Proteus penneri ATCC 35198]
          Length = 294

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 93/246 (37%), Positives = 134/246 (54%), Gaps = 4/246 (1%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           I+  + +EY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVHA  QV
Sbjct: 26  IKIALGVEYDGSRYYGWQRQNEVRSVQERLEKALSQVANEPISVFCAGRTDAGVHATGQV 85

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQ 120
            HF+             +N +L     I++  +  V   FHARFSA  R Y Y I   R 
Sbjct: 86  VHFETTAHRKDPAWTMGVNTHLPAD--IAVRWVKTVADDFHARFSATARRYRYVIFNHRY 143

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
            P  L  G        LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V+ +
Sbjct: 144 RPAILSSGVTHF-HYPLDAERMHQAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVSRY 202

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G+ + + + A +F+H  +R+ VGSL  +G G    T + + L  +DR +    A   GLY
Sbjct: 203 GDYVVVDIKANAFVHHMVRNIVGSLLEIGCGNQDITWMAELLALKDRTKAAATAKANGLY 262

Query: 241 FDSVEY 246
             SV+Y
Sbjct: 263 LVSVDY 268


>gi|330878235|gb|EGH12384.1| tRNA pseudouridine synthase A [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 274

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/251 (38%), Positives = 133/251 (52%), Gaps = 15/251 (5%)

Query: 3   RYCMIIEYNGSGYFGWQRQKNGS-SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           R  + +EY GS Y GWQRQ +G  ++Q ++E A+  V    V +  AGRTD+GVHA  QV
Sbjct: 8   RIALGVEYKGSRYCGWQRQASGVLTVQETLEDALSKVAASPVSLMCAGRTDAGVHACGQV 67

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD      ++ WV       + A + +   +S+    ++   FHARF AI R Y Y I
Sbjct: 68  VHFDTQAERSLKAWV-------MGANINLPHDVSVSWAKVMPATFHARFKAIARRYRYVI 120

Query: 117 ITRQ-APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHF 175
              Q  P  L +   W   + LD E M  AA++LVG HDF+ FR+  CQA SPI+ + H 
Sbjct: 121 YNDQIRPAHLNQEITW-NHRPLDVERMAQAAEYLVGTHDFSAFRAGQCQAKSPIKQLHHL 179

Query: 176 DVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAP 235
            V   G +I I V A +FLH  +R+  G L  +G G+         L+++ R+  G  A 
Sbjct: 180 RVTRHGKMIVIDVRANAFLHHMVRNIAGVLMTIGAGERPVEWARDVLESRVRRTGGVTAH 239

Query: 236 PEGLYFDSVEY 246
           P GLY   VEY
Sbjct: 240 PYGLYLVQVEY 250


>gi|16761293|ref|NP_456910.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29141011|ref|NP_804353.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|56412735|ref|YP_149810.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|62180940|ref|YP_217357.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|161612896|ref|YP_001586861.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|167549625|ref|ZP_02343384.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|168229744|ref|ZP_02654802.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168237394|ref|ZP_02662452.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|168242494|ref|ZP_02667426.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|168465920|ref|ZP_02699790.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|168817894|ref|ZP_02829894.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|194443793|ref|YP_002041632.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194450234|ref|YP_002046424.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194471784|ref|ZP_03077768.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194734499|ref|YP_002115439.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197248953|ref|YP_002147329.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197361669|ref|YP_002141305.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|198245997|ref|YP_002216441.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|200388490|ref|ZP_03215102.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204929209|ref|ZP_03220352.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205353481|ref|YP_002227282.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207857786|ref|YP_002244437.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|213022210|ref|ZP_03336657.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
 gi|213161334|ref|ZP_03347044.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
 gi|213426977|ref|ZP_03359727.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213646800|ref|ZP_03376853.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|213852689|ref|ZP_03382221.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
 gi|224583142|ref|YP_002636940.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|238912353|ref|ZP_04656190.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|289827487|ref|ZP_06546099.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|24212558|sp|Q8Z500|TRUA_SALTI RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|62901206|sp|Q5PCV6|TRUA_SALPA RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|81309634|sp|Q57LY6|TRUA_SALCH RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|189030141|sp|A9N476|TRUA_SALPB RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238689938|sp|B5BCH8|TRUA_SALPK RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238690009|sp|B5EZQ2|TRUA_SALA4 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238690247|sp|B4TBN7|TRUA_SALHS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238690344|sp|B5FPL2|TRUA_SALDC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238690447|sp|B5R349|TRUA_SALEP RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238690504|sp|B5RCJ3|TRUA_SALG2 RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238693568|sp|B4SZP0|TRUA_SALNS RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|238693647|sp|B4TQA4|TRUA_SALSV RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|254764863|sp|C0PZZ5|TRUA_SALPC RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|25292042|pir||AF0802 pseudouridylate synthase (EC 4.2.1.70) - Salmonella enterica subsp.
           enterica serovar Typhi (strain CT18)
 gi|16503592|emb|CAD07600.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29136636|gb|AAO68202.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|56126992|gb|AAV76498.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|62128573|gb|AAX66276.1| pseudouridylate synthase I [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|161362260|gb|ABX66028.1| hypothetical protein SPAB_00602 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194402456|gb|ACF62678.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194408538|gb|ACF68757.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194458148|gb|EDX46987.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194710001|gb|ACF89222.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|195631471|gb|EDX50031.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|197093145|emb|CAR58589.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|197212656|gb|ACH50053.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197289616|gb|EDY28979.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|197940513|gb|ACH77846.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|199605588|gb|EDZ04133.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204321753|gb|EDZ06952.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205273262|emb|CAR38227.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205325206|gb|EDZ13045.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205335762|gb|EDZ22526.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|205338670|gb|EDZ25434.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|205344778|gb|EDZ31542.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|206709589|emb|CAR33934.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|224467669|gb|ACN45499.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|320086803|emb|CBY96575.1| pseudouridylate synthase I [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
 gi|322617114|gb|EFY14020.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322617581|gb|EFY14480.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322624790|gb|EFY21619.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322630340|gb|EFY27110.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322634520|gb|EFY31253.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322639231|gb|EFY35923.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322640094|gb|EFY36761.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322645687|gb|EFY42211.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322652051|gb|EFY48414.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322656223|gb|EFY52520.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322659375|gb|EFY55622.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322665835|gb|EFY62018.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322669927|gb|EFY66068.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322673912|gb|EFY70009.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322678671|gb|EFY74727.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322683535|gb|EFY79549.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322687610|gb|EFY83580.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|322715420|gb|EFZ06991.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
 gi|323193556|gb|EFZ78761.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323198463|gb|EFZ83565.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323204575|gb|EFZ89578.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323208487|gb|EFZ93426.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323213625|gb|EFZ98414.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323218340|gb|EGA03050.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323220106|gb|EGA04572.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323224520|gb|EGA08802.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323232335|gb|EGA16438.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323235632|gb|EGA19716.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323241209|gb|EGA25245.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323244951|gb|EGA28953.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323250070|gb|EGA33964.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323253854|gb|EGA37679.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323254991|gb|EGA38782.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323259823|gb|EGA43455.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323264157|gb|EGA47664.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323270855|gb|EGA54293.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
 gi|326624193|gb|EGE30538.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326628574|gb|EGE34917.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
          Length = 270

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  ALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLA 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHYY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLLEVGAHNQPESWIAELLAARDRTLAAATAKAEGLYLVAVDY 252


>gi|16765695|ref|NP_461310.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|167993057|ref|ZP_02574152.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|168261608|ref|ZP_02683581.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|197263425|ref|ZP_03163499.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|24212561|sp|Q8ZNB9|TRUA_SALTY RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|16420911|gb|AAL21269.1| pseudouridylate synthase I [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|197241680|gb|EDY24300.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|205328800|gb|EDZ15564.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|205349584|gb|EDZ36215.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|261247574|emb|CBG25401.1| Pseudouridine synthase I [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267994470|gb|ACY89355.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301158926|emb|CBW18439.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312913359|dbj|BAJ37333.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321222930|gb|EFX48001.1| tRNA pseudouridine synthase A ; tRNA Psi38, Psi39 and Psi40
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. TN061786]
 gi|323130701|gb|ADX18131.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|332989301|gb|AEF08284.1| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 270

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 129/240 (53%), Gaps = 4/240 (1%)

Query: 8   IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLV 67
           IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   QV HF+  
Sbjct: 16  IEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPINVFCAGRTDAGVHGTGQVVHFETT 75

Query: 68  REWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIIT-RQAPLALE 126
                      +NA L     I++  +  V   FHARFSA  R Y Y I   R  P  L 
Sbjct: 76  ALRKDAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLA 133

Query: 127 KGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEI 186
           KG      + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   G  + +
Sbjct: 134 KGVTHYY-EPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVV 192

Query: 187 RVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEY 246
            + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY  +V+Y
Sbjct: 193 DIKANAFVHHMVRNIVGSLLEVGAHNQPESWIAELLAARDRTLAAATAKAEGLYLVAVDY 252


>gi|312135434|ref|YP_004002772.1| tRNA pseudouridine synthase a [Caldicellulosiruptor owensensis OL]
 gi|311775485|gb|ADQ04972.1| tRNA pseudouridine synthase A [Caldicellulosiruptor owensensis OL]
          Length = 244

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 90/241 (37%), Positives = 134/241 (55%), Gaps = 2/241 (0%)

Query: 6   MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFD 65
           + IEY+G+GYFGWQ+Q N  +IQG+IE+AI  +TGE V + G+GRTD GVHAL Q A+F 
Sbjct: 6   LTIEYDGTGYFGWQKQPNKKTIQGTIEEAIKKLTGEEVNLIGSGRTDRGVHALNQKANFK 65

Query: 66  LVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLAL 125
              +        ALN+ L     IS+ +   V   F AR+SA +++Y Y I  +++  AL
Sbjct: 66  TSSKIPTDKFPLALNSVL--PGDISVKDAVEVPLDFSARYSAKQKTYKYLIYNKKSRPAL 123

Query: 126 EKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIE 185
            +  A+  P  LD + M+ A ++ +G +DF +F S   +A + IR I +  +      I 
Sbjct: 124 LRNYAYYYPYELDVDAMQRACEYFIGEYDFKSFCSADSEAKTTIRHIYNAYLTFENECIA 183

Query: 186 IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE 245
           I + A  FL+   R   G++  VG GK    D+   ++++DR   G   PP GLY   V 
Sbjct: 184 IYITANGFLYNMARIIAGTILDVGAGKLKPMDIPLIIESKDRTLAGKTLPPWGLYLVDVV 243

Query: 246 Y 246
           Y
Sbjct: 244 Y 244


>gi|262276338|ref|ZP_06054147.1| tRNA pseudouridine synthase A [Grimontia hollisae CIP 101886]
 gi|262220146|gb|EEY71462.1| tRNA pseudouridine synthase A [Grimontia hollisae CIP 101886]
          Length = 264

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/252 (38%), Positives = 138/252 (54%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           +R  + +EY+GS ++GWQRQ+   S+Q  +EKA+  +  + V V  AGRTD+GVH   QV
Sbjct: 1   MRIALGVEYDGSQFYGWQRQREVPSVQEHLEKALSKIANQPVEVQCAGRTDAGVHGTGQV 60

Query: 62  AHFDL-----VREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRI 116
            HFD+     +R W        +N +L   DTI++     V  +FHARFSA  R Y Y I
Sbjct: 61  VHFDIEGSRPLRAW-----TMGVNTHL--PDTIAVRWAKEVPDEFHARFSATARRYRY-I 112

Query: 117 ITRQA--PLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
           I   A  P  L  G +      LD   M  A Q+L+G +DFT+FR++ CQ+ SP R + H
Sbjct: 113 IYNHALRPGILRHGVS-HYHGELDETLMHEAGQYLLGENDFTSFRAVQCQSKSPWRNVHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  + I + A +F+H  +R+  GSL +VG  +     ++  L+A+DR      A
Sbjct: 172 INVTRQGRFVIIDIKANAFVHHMVRNITGSLIVVGRKEQKPEWIKWLLEAKDRNLAAATA 231

Query: 235 PPEGLYFDSVEY 246
             EGLY   VEY
Sbjct: 232 KAEGLYLVEVEY 243


>gi|293390012|ref|ZP_06634346.1| tRNA pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290950546|gb|EFE00665.1| tRNA pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 261

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/252 (36%), Positives = 138/252 (54%), Gaps = 16/252 (6%)

Query: 2   IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQV 61
           ++  + +EY+G  YFGWQRQ+  +SIQ  +E+AI ++  E + +  AGRTDSGVHA  QV
Sbjct: 1   MKIALGVEYDGKHYFGWQRQEKVASIQAELERAISVIANEDIGIFCAGRTDSGVHAAGQV 60

Query: 62  AHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQA 121
            HF+   +         +NA L   D I++    +V+  FHARFSA  R Y Y       
Sbjct: 61  IHFETTAQRPEKAWSFGVNANL--PDDIAVRWAKVVEDDFHARFSATARRYRYI------ 112

Query: 122 PLALEKGRAWLIPK-------SLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDH 174
            L   K R+ ++P+        LD + M  A Q L+G +DF++FR+  CQ+++P R + H
Sbjct: 113 -LYCNKLRSAILPQGVTHCHLELDHQLMHDAGQALLGENDFSSFRAAQCQSNTPWRNVHH 171

Query: 175 FDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLA 234
            +V   G  I + + A +F+H  +R+ VGSL  VG        ++  L+ +DR    P A
Sbjct: 172 LNVTRQGQYIIVDIQANAFVHHMVRNIVGSLIEVGCCNQPVEWMKWLLEQKDRALAAPTA 231

Query: 235 PPEGLYFDSVEY 246
            PEGLY  +V Y
Sbjct: 232 KPEGLYLVNVIY 243


>gi|222529670|ref|YP_002573552.1| tRNA pseudouridine synthase A [Caldicellulosiruptor bescii DSM
           6725]
 gi|254789602|sp|B9MKC1|TRUA_ANATD RecName: Full=tRNA pseudouridine synthase A; AltName: Full=tRNA
           pseudouridylate synthase I; AltName: Full=tRNA-uridine
           isomerase I
 gi|222456517|gb|ACM60779.1| tRNA pseudouridine synthase A [Caldicellulosiruptor bescii DSM
           6725]
          Length = 244

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 89/241 (36%), Positives = 134/241 (55%), Gaps = 2/241 (0%)

Query